Anae didn't get along with Brandon Doman and to a lesser degree Lance Reynolds. I believe Doman was undermining Anae with the hope of taking over his position at OC. The fact that Bronco asked Anae to resubmit his application was a minor thing.
When Doman's offense turned into a train wreck, Bronco realized he should have done more to retain Anae. It is absolutely clear why Anae didn't retain Doman on his offensive staff when he came back to BYU. Would you keep on your staff someone who was a major factor in your leaving BYU and someone who was not loyal to you? I infer that Brandon wanted to stay on and go back to his old position as quarterbacks coach. I really can't understand it, if Doman, in fact, is still upset that he wasn't kept on the BYU staff in a lower position. From my position, it seems a little hypocritical to expect someone to show you mercy when you didn't show mercy and were instrumental in getting him out.