Not common but not really rare either. Easy fix tho. Get a 3-4 in. piece of 3/8 in. dowel rod and glue a disc of 280 to 400 grit black sandpaper to the end. When it's dry, trim off any excess and then press the paper lightly against the bolt face while spinning the dowel a few times to remove the raised burr. Any other method might radius the pin hole and that wouldn't be a good idea.
It would be ideal to disassemble the bolt before you start and then flush any residual abrasive grit out before reassembling it.