If the cylinder notches have displaced metal, peen it back into place, making sure the bolt still fits the resulting notch. It will not affect alignment. If the bolt has slightly rounded edges, replace it. A trick that can help in extreme cases is to alter the bolt so that it rises further.
If you have to manipulate the cylinder to create the problem, then it is much ado about nothing. Don't do that, and everything will be fine!
If you have to manipulate the cylinder to create the problem, then it is much ado about nothing. Don't do that, and everything will be fine!