My 1040 is showing my 1099-R nontaxable income as taxable which has made the amount I owe skyrocket. Do I need to file an amendment to fix or will the IRS catch it?

Have you already filed your Federal 1040 tax return?  Has it been accepted?

If your Federal 1040 tax return has been filed and accepted, you will likely have to amend your Federal tax return by filing an amended tax return. It may happen, but I would not count on the IRS correcting the issue.

If your Federal 1040 tax return has been filed and rejected, you will be able to enter the TurboTax software and correct the error before filing your Federal 1040 tax return.

Amended tax returns will not be available before February 23. See forms availability here.

If you used TurboTax Online, simply log in to your account and select Amend a return that was filed and accepted.

If you used the CD/download product, sign back into your return and select Amend a filed return. 

You must file a separate Form 1040-X for each tax return you are amending.

See also this TurboTax Help.