The member of the congregation has to follow his imam with regard to matters that are subject to ijtihaad
Question

                Is it correct to join them in this or should we pray witr seperately?.
Praise be to Allah.
    Firstly: 

    It is narrated that the Prophet  (peace and blessings of 
    Allaah be upon him) forbade making Witr prayer resemble Maghrib. See 
    question no. 38230. 

    The scholars differed concerning the case where the imam does 
    something in the prayer that the person praying behind him thinks is not 
    allowed, or if the imam omits to do something that the person praying behind 
    him thinks is obligatory – should he follow him or not? 

    Shaykh al-Islam Ibn Taymiyah (may Allaah have mercy on him) 
    mentioned the scholarly dispute and favoured the view that he should follow 
    the imam so long as the matter is something that is subject to ijtihaad. 

    He said in al-Fataawa al-Kubra (2/117): 

    They disputed regarding a case where the imam omits something 
    that the person praying behind him thinks is obligatory, such as if he omits 
    to recite the Basmalah, and the person praying behind him thinks that it is 
    obligatory, or he touches his penis and does not do wudoo’, and the person 
    praying behind him thinks that wudoo’ is obligatory in that case, or he 
    prays wearing tanned leather from an animal that died naturally, and the 
    person praying behind him thinks that tanning does not render the animal 
    skin pure, or he is treated with cupping and does not do wudoo’ after that, 
    and the person praying behind him thinks that one should do wudoo’ after 
    cupping – the definitive correct view is that the prayer of the person who 
    prays behind an imam is valid, even if the imam makes a mistake, because it 
    is narrated in al-Saheeh that the Prophet  (peace and blessings 
    of Allaah be upon him) said: “They lead you in prayer and if they get it 
    right, it is for you and for them, and if they make a mistake it is for you 
    and against them.” Similarly if the person praying in congregation follows 
    someone who recites qunoot in Fajr or Witr, he should recite qunoot with 
    him, whether before or after bowing, and if he does not usually recite 
    qunoot, then he should not recite qunoot with him. If the imam thinks that 
    something is mustahabb but the people praying behind him do not think it is 
    mustahabb, and he omits it for the sake of harmony, he has done well. An 
    example of that is Witr: there are three scholarly opinions concerning it: 

    1 – That it can only be offered as three rak’ahs joined 
    together, like Maghrib, as was the view of some of the people of Iraq;

    2 – That it can only be a single rak’ah offered separately 
    from those that come before it, as was the view of some of the people of the 
    Hijaaz;

    3 – That both are permissible, as appears to be the view of 
    al-Shaafa’i, Ahmad and others, and this is the correct view.  

    If these people are of the view that it should be separate 
    from whatever comes before, and if the imam is of the view that it should be 
    separate, but the people praying behind him favour the view that Witr should 
    be like Maghrib, and he goes along with them in the interests of harmony, 
    then he has done well, as the Prophet  (peace and blessings of Allaah be 
    upon him) said to ‘Aa’ishah: “Were it not that your people are new in Islam, 
    I would have knocked down the Ka’bah, made its door level with the ground, 
    and I would have given it two doors, one through which the people could 
    enter and another through which they could exit.” But he chose to forego 
    that which he thought was better, so as not to upset the people. 

    End quote. 

    He also said in al-Fataawa al-Kubra (2/320): 
If the imam does not do 
    something that the person praying behind him thinks is obligatory there are 
    two opinions concerning that. The more correct of them is that the prayer of 
    the person praying behind the imam is valid. This is the view of Maalik and 
    the clearer of the two reports narrated from Ahmad concerning such matters. 
    This is also narrated from al-Shaafa’i, because he used to pray behind the 
    Maalikis who do not recite the Basmalah, but his view is that it is 
    obligatory to recite it. The evidence for that is the report narrated by 
    al-Bukhaari and others, that the Prophet  (peace and blessings of Allaah 
    be upon him) said: “They lead you in prayer and if they get it right, it is 
    for you and for them, and if they make a mistake it is for you and against 
    them.” So he said that the imam’s mistake counts against him but not against 
    the one who prays behind him. So if the imam’s view is the correct one in 
    such cases, then there is no dispute; if he is mistaken then his mistake 
    affects him alone. The one who thinks that the person praying behind the 
    imam should not follow him in that says: the person praying behind the imam 
    thinks that his imam’s prayer is invalid. Shaykh al-Islam said: That is not 
    the case, rather he thinks that the imam is praying on the basis of ijtihaad 
    or taqleed; if he gets it right then he will have two rewards and if he gets 
    it wrong he will still have one reward. 
End quote. 
And he said in 
    al-Ikhtiyaaraat al-Fiqhiyyah (70): 
If the imam does 
    something that is forbidden in the eyes of the one who is praying behind him 
    but not in his own eyes, which is a matter that is subject to ijtihaad, then 
    his prayer offered behind him is valid. This is the well-known view narrated 
    from Ahmad. And he said: The reports narrated from Ahmad may appear 
    contradictory but they are not, rather the apparent meaning is that in every 
    case where a person is certain that the imam has made a mistake,  then he 
    has to repeat the prayer, and in every case  where there is no such 
    certainty, then he should not repeat the prayer. This is what is indicated 
    by the Sunnah and the reports. There is a well-known dispute on this point 
    among the scholars. 
So you have to follow the 
    imam, because this is a matter of ijtihaad concerning which the imams 
    differed. 
If you can advise the 
    imam and explain the Sunnah to him, with evidence, then this is what you 
    should do. 
And Allaah knows best.