There are lots of ways in which Ender provoked Bonzo, which of course led to their conflict and, as we find out towards the end of the novel, their final face-off in the showers where Ender actually kills Bonzo. Mostly, of course, it is Ender's talent and intelligence that provokes Bonzo, who recognises his own lack of ability in the face of Ender's skill. However, if we had to pick one incident in particular, it would be when Ender deliberately defies the orders of Bonzo by firing during the game between Salamander and Leopard. He had already frozen his legs and appeared to be just another frozen soldier, but when Salamander had been defeated, and Leopard were starting the process of winning the game, Ender, with the element of surprise, managed to freeze enough men to save Salamander from an outright defeat and force a draw. Note Bonzo's response:
Everyone in Leopard Army assumed that it had been a strategy of Bonzo's, to leave a man till the last minute. It didn't occur to them that little Ender had fired against orders. But Salamander Army knew. Bonzo knew, and Ender could see from the way his commander looked at him that Bonzo hated him for rescuing him from total defeat.
It is this incident that results in Ender's trade from Salamander to Rat Army and ensures that the animosity Bonzo has for Ender is permanent.