In a December 2019 interview in the New York Times, Brad Pitt says this about "12 Monkeys":
I nailed the first half of “12 Monkeys.” I got the second half all wrong. That performance bothered me because there was a trap in the writing. It’s not the writing’s fault, but it was something that I couldn’t figure out. I knew in the second half of the film I was playing the gimmick of what was real in the first half — until the last scene — and it bugged the [expletive] out of me.
The interview doesn't elaborate further. I can't quite figure out what Pitt is referring to, though; what he means by "trap" or "playing the gimmick". My best guess is that he is talking about Cole's incorrect memory of Jeffrey Goines being at the airport instead of Dr. Peters. But that scene has Brad Pitt in such a short amount of screen time it feels strange that Pitt would be unhappy about his performance there.
Or possibly he is talking about the scene where Jeffrey tells Cole that Cole gave him the idea of releasing a virus and he has no relation with the Army of the 12 Monkeys, when in reality he has nothing to do with the virus and is the founder of the Army? If so, I'm not seeing what Pitt doesn't like about his performance there either.