We too had scratched window panes when we were closing on our house. At first the builder said it 'just happens', but we wouldn't back down and eventually got all the panes replaced and the front door as well, which was also scratched.
He told me later that most builders have a contingency for scratched glass, damage to sanitary ware etc.
It's up to you, but I would dig my heels in and say it's not acceptable and you want them replaced.
You could perhaps, as AKA suggested, compromise and overlook some smaller scratches in order to get the badly scratched ones replaced.