I think you handled it really well - same thing happened to me as a 5th grader where I turned in a couple of magazines and got actual mail (WAY before email) telling me I owed them $10 for a magazine that clearly said $1.99 on the cover. I'd have paid the 2 bucks just be done with it, but (like you) the injustice of paying more for something won out. I walked back to the shelf, saw the magazine and brought it back to the front.

"I think you may have accidentally missed this when you checked in my books the other day"

Case closed, fine cancelled.