No, if box 7 of the 1099-R is code G, then there shouldn't be a problem. The IRS has received a copy of your 1099-R, so they know what that it was rolled over.
There is one entry on Form 1040, line 16a that would show the entry for all pension distributions (taxable or otherwise), but it shouldn't affect the rest of your return.
The addition of a 1099-R, Box 7, code G would yield a no change Amended Return.