Be very careful interpreting what these notes mean.

I believe that Priestap was having problems with the way that the FBI was handling the investigation. His notes state that the goal (pre interview) is to resolve the case. Then in the Afterwards section he states:

I THOUGHT ON IT LAST NIGHT AND I THINK WE SHOULD RETHINK THIS. He then questions what the goal is. He is questioning the FBI methods of conducting the interview because he believes that they are trying to set up Flynn. He then says to protect the institution by NOT PLAYING GAMES.