Specifically his action stuff. Some felt he came off much weaker than he should've. For me, it's bothersome in one particular scene where Cap can't seem to take out a goon with a gun to pull a lever. Putting the characters through the grinder is fine, but I found this troublesome on a story level, since in my mind this should've really been the scene where Cap fully earns Stark's respect to make him step aside for the climax as leader, but instead Stark does all the heavy lifting, including saving Cap by knocking the goon on his ass.
As far as Stark knows, he had to order Cap to meet him outside and pull a lever while he did all the calculating and physical labor, then had to save his ass from a random henchman, all the while Cap has a gun that he can't seem to fire. There's not really a strong segue from him disrespecting Steve to him asking to be ordered around by him.
In fact, that's my only major beef with the first movie. Not all the dumb minute details like the Chitauri dropping dead in unison or "not enough Hawkeye" or anything, since it has direct impact on the story in a negative way for me.