What does it mean when a guy says he does not feel like he is in control when he is with you?

He wants to be in charge. Maybe HE wants to pick the movie, or the restaraunt, or where he wants to put his hands. He probably means that you are too controlling, not to be taken offensively. He just wants to have more of a say in the relationship.

It could also mean that that he has such a strong crush on you, that he physically loses control of himself when he is near you. Meaning that he wants to touch you and be more physical with you than might be appropriate.