Either Charles is damaging it when he passes by or one of the Cultists with shotgun.

dang

Originally posted by Shovel Mann:

I was in nightmare mode, when Charles appears, he'll damage my train, even when im outside of the train IN THE FIRST PLACE,(this has happened multiple times before I was able to record it btw.)
https://youtu.be/-OgznqNLGZQ

Best advice I can give you is make sure you have a fair distance between you and the train so when Charles does spot you, they're a higher chance he won't attack your train and just focus on you. Additionally if he gets close to the train then come out of your hiding spot a tad to draw his attention to you.

It's not a bug by any means, I think the dev made it like that intentionally

Charls probably damnages the train slightly when bumping into it. It happened to me when I was off the train hiding in a house. Same thing with the cultists, there shotguns can actually damnage the train as well.