There is no contradiction between the description of the Qur’an as being clear and explained in detail, and the appearance of the huroof muqatta‘ah in it
Question

                Quranic verses are considered fussilat, that is explained in details in Surah Hud 11:1 and fussilat 41:3 but Huroof Muqomatats (qur'anic verses) meaning according to scholars are not explained by the prophet, that is not fussilat (which is contradictory). 

Since Qur'an cannot contradict itself, how can we reconcile both?
Praise be to Allah.
	There is no contradiction between the Qur’an being described 
	as clear and explained in detail, as Allah, may He be exalted, says 
	(interpretation of the meaning): 

	“We have (indeed) explained in 
	detail Our Ayât (proofs, evidences, verses, lessons, signs, Revelations, 
	etc.) for people who know” [ al-An 
	‘aam 6:97]

	“Certainly, We have brought them 
	a Book (the Qur’an) which We have explained in detail with knowledge, - a 
	guidance and a mercy to a people who believe”

	[al-A ‘raaf 7:52]

	and the huroof muqatta’ah [groups of letters that appear at 
	the beginning of some soorahs].

	Ibn Katheer (may Allah have mercy on him) said: 
	

	“We have (indeed) explained 
	in detail Our Ayât (proofs, evidences, verses, lessons, signs, Revelations, 
	etc.)” means: We have explained 
	them and clarified them.

	End quote from Tafseer al-Qur’an al-‘Azeem (3/305).

	There is no contradiction between that and the fact that the 
	Holy Qur’an contains the huroof muqatta‘ah at the beginning of some soorahs, 
	for several reasons:

	-1-

	The idea of being clear and explained in detail is applicable 
	to the Qur’an and to its soorahs and verses, in general, not to every single 
	word in it, which means that the idea of being explained in detail does not 
	rule out exceptions. The Holy Qur’an itself states that there are 
	exceptions, as is seen in the verse in which Allah, may He be glorified and 
	exalted, says (interpretation of the meaning):

	“It is He Who has sent down to 
	you (Muhammad (blessings and peace of Allah be upon him)) the Book (this 
	Qur’an). In it are Verses that are entirely clear, they are the foundations 
	of the Book [and those are the Verses of Al-Ahkâm (commandments), Al-Farâ'id 
	(obligatory duties) and Al-Hudud (legal laws for the punishment of thieves, 
	adulterers)]; and others not entirely clear. So as for those in whose hearts 
	there is a deviation (from the truth) they follow that which is not entirely 
	clear thereof, seeking Al-Fitnah (polytheism and trials), and seeking for 
	its hidden meanings, but none knows its hidden meanings save Allah. And 
	those who are firmly grounded in knowledge say: ‘We believe in it; the whole 
	of it (clear and unclear Verses) are from our Lord.’ And none receive 
	admonition except men of understanding”

	[Aal ‘Imraan 3:7].

	Shaykh Muhammad al-Ameen ash-Shinqeeti (may Allah have mercy 
	on him) said in al-‘Adhb an-Nameer (2/168):

	“it is He Who has sent down unto you the Book (the Qur’an), 
	explained in detail” [al-An ‘aam 6:114] 
	means: in it, beliefs are explained clearly; in it the truth is explained 
	and made distinct from falsehood, what is beneficial is made distinct from 
	what is harmful, what is good is made distinct from what is bad. In it Allah 
	explains: beliefs; halaal and haraam; what brings a person closer to Allah 
	and what leads to His Paradise; what takes a person further away from Allah 
	and incurs His wrath, and leads a person to His Hell; and He explains the 
	ultimate destiny of both groups; what He has prepared for His close friends 
	and what He has prepared for His enemies. All of that is explained in detail 
	in the Qur’an. Even though there are some ambiguous verses in the Qur’an 
	(those that are not entirely clear), they are to be understood in the light 
	of the clear verses, and their meanings are to be understood in the light of 
	the clear verses.

	As we mentioned above in Soorat Aal ‘Imraan regarding the 
	meaning of the verse (interpretation of the meaning): 
	“in it are Verses that 
	are entirely clear, they are the foundations of the Book” 
	[Aal ‘Imraan 3:7].

	What this means is that the clear (muhkam) verses are the 
	foundations of the book in the light of which anything that is unclear of 
	the ambiguous (mutashaabih) verses is to be interpreted and understood. This 
	is the meaning of the verse in which Allah says (interpretation of the 
	meaning):

	“it is He Who has sent down unto you the Book (the Qur’an), 
	explained in detail” [al-An‘aam 6:114].

	Explaining in detail is the opposite of speaking in general 
	terms; it means explaining and making clear. End quote.

	-2-

	The clear and detailed explanation of the verses of the Book 
	does not mean that the verses do not include general or ambiguous 
	statements, or verses that need to be interpreted, or verses that abrogate, 
	or statements that may have more than one meaning. In fact all these types 
	of verses exist in reality, but the Holy Qur’an – at the same time – 
	includes verses that explain in detail matters that are mentioned elsewhere 
	in general terms or are subject to interpretation or abrogation and the 
	like. It contains some verses which explain others, and there are verses 
	that explain what people need to know.

	Hence we may regard the scholars’ discussion of the meaning 
	of the huroof muqatta‘ah as being another detailed explanation, i.e., a 
	clarification thereof; so that there is no contradiction between the 
	existence of those letters and the description of the Qur’an as being the 
	book that is clear and explained in detail.

	The scholars said: If the Qur’an was all the same in its 
	level of clarity and ease of understanding its meanings, the scholars would 
	not have differed in their ways of interpreting and understanding it. But 
	Allah decreed that there should be people who would be raised in status 
	because of their knowledge, and that people would vary in their level of 
	knowledge; therefore their explanations varied, according to their level of 
	knowledge.

	End quote from ‘Aaridat al-Ahwadhi (1/124). 
	

	He also said:

	With regard to it all being described as beautifully put 
	together with the utmost conciseness and eloquence, using few words with 
	abundant meanings, it is as Allah, may He be glorified and exalted, said 
	concerning it (interpretation of the meaning): “a 
	Book, the Verses whereof are perfected (in every sphere of knowledge), and 
	then explained in detail” [Hood 
	11:1]. 
	

	With regard to it all being mutashaabih (parts of it 
	resembling other parts), because it discusses throughout these meanings that 
	have been explained in detail, without falling short, going to excess, 
	adding unnecessary detail or contradicting itself, it is as Allah, may He be 
	exalted, says (interpretation of the meaning):

	“Do they not then consider the 
	Qur’an carefully? Had it been from other than Allah, they would surely have 
	found therein many contradictions”

	[an-Nisa’ 4:82]

	“Allah has sent down the Best 
	statement, a Book (this Qur’an), its parts resembling each other (in 
	goodness and truth)”

	[az-Zumar 39:23].

	With regard to its verses being of two types, some of which 
	are clear (muhkam) and some are ambiguous (mutashaabih), what 
	is meant is that some verses are clear in meaning and others are subtle in 
	meaning. If our Lord, may He be glorified, had so willed, He could have made 
	all its verses equal in clarity. But He decreed that among people there 
	would be some who are knowledgeable and others who are ignorant, some who 
	are well-versed in knowledge and others who are lacking therein, and He made 
	them vary with regard to their level of understanding as He, may He be 
	glorified and exalted, said (interpretation of the meaning):

	“Allah will exalt in degree 
	those of you who believe, and those who have been granted knowledge”

	[al-Mujaadilah 58:11].

	Here Allah, may He be glorified and exalted, tells us that He 
	raises people in status by means of their faith, and raises them further by 
	means of their knowledge. The one who does not understand its interpretation 
	may limit himself to believing in it and accepting its meaning as Allah 
	intended it to mean.

	The one who is well versed in knowledge may examine it and 
	understand the ambiguous (mutashaabih) verses in the light of the 
	clear (muhkam) verses and whatever possible interpretation of the 
	ambiguous verses is in accordance with the meaning of the clear verses, he 
	may adopt that interpretation, and whatever interpretation contradicts it, 
	he may ignore it. If it is possible, he may find a report from the Messenger 
	of Allah (blessings and peace of Allah be upon him) to support the 
	conclusion he reached.

	End quote from al-Qabas fi Sharh Muwatta’ Maalik ibn Anas 
	(p. 1058)

	-3-

	The huroof muqatta‘ah are simply there to begin the soorahs, 
	like something to alert the reader at the beginning. They are not 
	necessarily connected to the topics discussed in the chapters, or the topics 
	of the verses that the Qur’an speaks of and describes as being clear and 
	explained in detail, based on the fact that the description of clarity and 
	detail most often comes directly after the huroof muqatta‘ah. Allah, may He 
	be exalted, says (interpretation of the meaning):

	“Alif-Lâm-Râ. [These letters are one of the miracles of the 
	Qur’an and none but Allah (Alone) knows their meanings]. (This is) a Book, 
	the Verses whereof are perfected (in every sphere of knowledge), and then 
	explained in detail from One (Allah), Who is All-Wise Well-Acquainted (with 
	all things)”

	[Hood 11:1]

	“Hâ­Mîm [These letters are one of the miracles of the Qur’an, 
	and none but Allah (Alone) knows their meanings.] 

	A revelation from (Allah) the Most Gracious, the Most 
	Merciful. 

	A Book whereof the Verses are explained in detail — a Qur’an 
	in Arabic for people who know”

	[Fussilat 41:1-3].

	If this was a contradiction, it would not be like this, which 
	could be easily avoided by any human being, let alone the Lord of mankind, 
	to Whom belongs absolute perfection.

	Therefore it is clear that what is referred to when the 
	Qur’an is described as being explained in detail is the verses that discuss 
	the main objectives of the Holy Qur’an, which is to explain Allah’s Oneness 
	in His Lordship, His divinity, and His names and attributes; to deny that He 
	has any partner; to state that absolute rulership belongs to Him alone, may 
	He be glorified and exalted; and similar basic concepts that the Prophet 
	(blessings and peace of Allah be upon him) was sent to correct among the 
	disbelievers of Quraysh. But if some verses were not made explained in 
	detail, such as verses that speak of historic events, matters of the unseen, 
	or issues having to do with rules and regulations, there is nothing wrong 
	with that.

	The wisdom behind that is so as to leave room for putting 
	effort into understanding the verses (ijtihaad) and to create motives for 
	academic research and discussion by those who are well-versed in knowledge. 
	This is one of the greatest reasons for there being some ambiguous verses in 
	the Qur’an and Sunnah.

	-4-

	It may also be said that what is meant by the Qur’an being 
	explained in detail is that it is clear in the minds of the well-versed 
	scholars, and even the huroof muqatta‘ah and the ambiguous (mutashaabih) 
	verses are within the realm of their thinking and understanding. 
	

	Based on that, there is no contradiction at all. With regard 
	to those who are not well-versed in knowledge, the verses that are not clear 
	to them are many, not just the huroof muqatta‘ah, as the Prophet (blessings 
	and peace of Allah be upon him) said: “That which is halaal is clear and 
	that which is haraam is clear, and between them are doubtful matters which 
	many people do not understand.” Narrated by al-Bukhaari (52) and Muslim 
	(1599). So the ambiguity and lack of clarity is not something that affects 
	the scholars; rather it is something that affects the ordinary people only.

	Shaykh al-Islam Ibn Taymiyah (may Allah have mercy on him) 
	said:

	Ambiguity or lack of clarity is something relative. Something 
	may be unclear to one person, but not to others. But there are some verses 
	that are clear and there is no ambiguity in them for anyone. With regard to 
	the ambiguous verses, once the meaning is known, they become no longer 
	ambiguous. Rather everything in the Qur’an is clear, as Allah, may He be 
	exalted, says (interpretation of the meaning):

	“(This is) a Book, the Verses whereof are perfected (in every 
	sphere of knowledge), and then explained in detail”

	[Hood 11:1].

	End quote from Majmoo‘ al-Fataawa (13/144).

	-5-

	This confusion only arises if we understand the explaining in 
	detail of the Qur’an as indicating that it is clear in its meanings, as was 
	narrated above from Ibn Katheer. But if we understand the word fussilat 
	(explained in detail) in accordance with other interpretations, then it will 
	become clear that there is no contradiction with the huroof muqatta‘ah.

	Describing the Qur’an as mufassil (explained in detail) does 
	not mean that the meanings and interpretation are clear, according to many 
	scholars. Rather what it means is that it makes a clear distinction between 
	truth and falsehood, or between halaal and haraam. And there are other views 
	and interpretations. So if we interpret being explained in detail in this 
	manner, then there is no contradiction between the Qur’an being explained in 
	detail and the presence of the huroof muqatta‘ah at the beginning of some 
	soorahs, because the presence of these letters does not affect the fact that 
	the Qur’an makes truth distinct from falsehood, and halaal distinct from 
	haraam.

	Imam al-Maawardi (may Allah have mercy on him) said:

	Then he said regarding the verse (interpretation of the 
	meaning), “We 
	have (indeed) explained in detail Our Ayât (proofs, evidences, verses, 
	lessons, signs, Revelations, etc.) for people who know” 
	[al-An‘aam 6:97]:

	There are four interpretations of what is meant by it being 
	explained in detail. They are: 

	1.
	
	its meanings are 
	explained in detail so that so that it becomes clearand not ambiguous;

	2.
	
	it makes the one 
	who is truthful distinct from the liar;

	3.
	
	it makes truth 
	distinct from falsehood, and guidance distinct from misguidance, as was the 
	view of al-Hasan;

	4.
	
	it makes 
	commands distinct from prohibitions, what is recommended distinct from what 
	is prohibited, and what is halaal distinct from what is haraam.

	End quote from an-Nukat wa’l-‘Uyoon (2/160).

	He (may Allah have mercy on him) also said:

	With regard to the verse (interpretation of the meaning), “A 
	Book whereof the Verses are explained in detail” [Fussilat 1:3], there 
	are five interpretations:

	1.
	
	that it is 
	explained and interpreted, as was suggested by Mujaahid;

	2.
	
	that it was 
	explained by mentioning promises and warnings, as was suggested by al-Hasan;

	3.
	
	that it was 
	explained by mentioning the reward and punishment, as was suggested by 
	Sufyaan;

	4.
	
	that it was 
	explained by distinguishing between halaal and haraam, obedience and 
	disobedience, as was suggested by Qataadah;

	5.
	
	that it was 
	explained with regard to Muhammad (blessings and peace of Allah be upon 
	him), thus judgement was passed between him and those who opposed him, as 
	was suggested by ‘Abd ar-Rahmaan ibn Zayd.

	End quote from an-Nukat wa’l-‘Uyoon, 5/167

	And Allah knows best.