I have this weird headcanon that crazy!Fred Bonaparte doesn’t like birds because they tend to fly and roost above his head. Seeing as how his memory version of Napoleon is so ridiculously short, I figure he’d be carting around a few height issues, even though Fred himself is the tallest character in the game. And being not quite so right in the head, I don’t think he’d distinguish them from anything else. He was kicking a teddy bear around like a game piece, after all.
Also it’s funny to imagine him marching around the asylum courtyard shouting at birds.