Question: If a player commits a *direct* free kick offence in their own penalty area, this results in a penalty kick instead of a direct free kick. However, if the offence is an *indirect* free kick offence, it remains as an indirect free kick [as shown here](https://www.youtube.com/watch?v=zPx5AUx0zhg).

What offences result in an indirect free kick?

Answer: 
Inside the penalty box, an indirect free kick, instead of a penalty, will be awarded

* if the goalkeeper controls the ball with his hands for more than six seconds.
* if the goalkeeper touches the ball with his hands after he has released it from his possession and before it has touched another player.
* if the goalkeeper handles a back pass.
* if the goalkeeper handles the ball directly from a throw-in taken by a team-mate
plays in a dangerous manner.

Sources: [This](http://www.seriousgoalkeeping.net/Tactics/FreeKicks/IndirectFreeKickInsideBox.aspx) and [this](http://news.bbc.co.uk/sport2/hi/football/rules_and_equipment/4200994.stm). More details about the procedure, positions and rules about indirect free kicks can be read [here](http://www.fifa.com/aboutfifa/footballdevelopment/technicalsupport/refereeing/laws-of-the-game/law/newsid=1290870.html).
Indirect free kicks in the box were quite common at all levels of the game until about 20 years ago. It is nearly always for "obstruction". The problem has been that players now deliberately obstruct, which can be seen as "reckless or excessively forceful", hence a direct free kick/penalty.
Referees tend to see all obstructions now as deliberate, leading to far more penalties (or calls for penalties from attackers deliberately barging into defenders to try to "win" a penalty) being given.
With more games televised there are more controversies about the awarding of pens, especially in "homer" situations. 
Unfortunately unless players begin to behave better (and stop cheating,) the obstruction rule will continue to lead to direct free kicks only.