Oh yes, I hope the Dev doesn't take it personal, but I think this is a problem too. It kinda breaks the line of thinking I guess. This is the only thing I would change in the game, everything else is lovely.
Yeah, it's kind of like when you're talking to someone and they say "Um" or "y'know" every other sentence. Especially in the script of the characters' thoughts, they should be eliminated. Someone might say "Hee hee" or chuckle as a verbal tick, but no one actually thinks it.