Bolt is popping up too soon and is peening the cylinder. This means the timing is bad.
- The tail of the bolt may be too short, which causes it to fall off too fast.
- Or the hand may be too short, causing the cylinder not to rotate fast enough before the bolt pops up.
- Or the stub on the hammer that operates the bolt is worn out, allowing the bolt's tail to fall off too fast.
- Or the sear (top of the trigger) is worn (too short) and thus the hammer has to over-rotate for it to engage each of the three notches.
BTW, do not file those marks off on your cylinder. I would use a punch and try to peen them back down.