If you're really careful and it's flared outward, you can probably get away with getting a small hammer and tapping it back into shape. However, I can't quite tell from your picture as the deformation on the lower hole looks to be more than just flared. I'd insert the fastener into the hole and pay careful attention as to where the gaps are before deciding to apply some DIY bodywork.
As an added precaution, you can line the fastener on your panel with some duct tape to give it a bit of extra "bite". A bit ghetto I know.
Your other alternative is to get the sheetmetal patched and to have new holes punched.