No, it is not a problem with TurboTax. You should have received two Forms 1099-R - one for the Roth Rollover and one for the Traditional Rollover. I would enter it as two different transactions - Forms 1099-R. It shouldn't cause any problems, as the IRS tends to look at things in total. Worst case scenario, as I see it, is that you get a letter from the IRS to which you would just need to respond to with an explanation and perhaps some documentation.
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