Peter loses it and lunges at Ben saying he won't let him steal his life. He says the tests were rigged and that Trainer is trying to play with his life. As they battle, MJ rushes to help but Pete half-turns and smashes her halfway across the room into a machine. Pete can't believe what he's done and runs for it, leaving MJ sobbing away.
Either way, it was in the heat of the moment when he was battling someone else. It's different than what Hank did.