Well from what I can gather, the Hulk that was unleashed on board the Helicarrier was out of control due to Loki managing to play with their minds using the staff that was left in the research bay. When they realised that Loki was targeting Banner and wanted to release the Hulk, Fury & Black Widow were urgently trying to remove him from the area. In the room peoples emotions, ego's and anxiety's were raised while they questioned each others motives, but this was all caused by Loki omitting some form of 'drug' like feeling from the staff.
A couple of things that back this I think are how Cap is easily convinced that SHIELD are up to something behind the scenes, when he tries to disregard this notion Banner & Stark easily turn his head and Cap goes off to find out whats going on alone, going against his usual Soldier character and breaking his orders. Also, the argument scene just before the explosion is filmed like a air born toxin / gas is attacking each of the Avengers and boosting the aggression towards one another. Best section of this argument to confirm this is with Thor, as the camera pans on his face (again like a toxin is attacking him) he says "You people are so petty, and tiny." - this line goes totally against his opinion of humans (which he was talking to Loki about just earlier in the film) and how he can relate to them, instead this line makes him sound like he is above them and acting more like a "God"!
That's my opinion on it all, and would give a valid reason for the Hulk outburst on the Helicarrier... Or maybe I shouldn't read too much into things
