Was he really crying? No, he wasn't crying, but he was going to. Tears were already forming in his eyes and he looked so sad. The pouting face and crossed arms clearly showed that he was offended.
At who? At you.
Why? You hit him on the back of the head with a notepad and then scolded him. But it was almost nothing, because you also called him a bad boy. Bokuto loved your praise so much, and didn't liked when you scolded him and especially called him that.
So why did you scold him and do all this? He was messing around during training. In fact, it was nothing surprising, but it distracted Kuroo and the other teams in principle, preventing them from concentrating. You didn't even know that Bokuto was sitting in the corner of the gym, offended and not talking to anyone.
Akaashi informed you about this, because you were their manger and the reason why Bokuto was in such a state.
When you approached him, you heard him sobbing softly, turned his back to you.