In The Avengers after falling from great height and blasting through the cage, Thor seems to have lost his control over the hammer, why did this happen?
I think it is not that he cannot do it, but that he is emotionally very much shaken and disappointed, since this is right after Loki tried to kill him (which is what that fall was supposed to do). What we see in that scene is hesitation, not failure.
In the next Thor scene, we see him lift it. He either can do so or cannot. There is no "he can lift it, but not summon it" for Mjölnir. And, obviously, he can lift it.
Thor can pick up his hammer he is just taking his time... at about 1 hour and 37 minutes the scenes catch up and come back to thor as everyone is "suiting up" and you see him pick the hammer up hold it in the air and lightning comes down and his armor seems to come down with the lightning. Here is a video of the scene:
This may have been confusing at first because Marvel split the scene up into a couple parts over a few minutes.
Also while I can't prove it I believe he could have summoned the hammer do his hand and just didn't want to or the directors decided that the scene had more of a more decisive and determined feel the way they did it. I believe this possible because the Marvel Cinematic Universe and the comics don't always agree.
Thor, being the God of Thunder, can summon his hammer as well as being the only guy to lift his hammer. The reason he cannot summon it after crashing on the field is because it needs to be energized by thunder to to do his bidding, without which it's just a heavy hammer. Only an electric force field around the hammer allows it to hover to him. That's why you see him walking towards the hammer, lifting it and energizing it by causing a thunderstorm to strike him and his hammer.