You should get the 1099-R corrected and then file to keep the possible negative repercussions from taking place.
The IRS will get the 1099-R, and that is what they will go by. They will look at the codes and see how the distributions should be handled and your return could possibly be changed causing a big tax liability as a result of the pre-tax showing up in the Roth which would trigger a taxable income amount.
If you see a potential problem with the return, it would be best to take care of it now rather than having to deal with issues later. It's easier to take care of a known issue now, before it becomes a major problem later.
