TurboTax has no way to know if the Form 1099-R for your pension distribution represents a distribution that is eligible for rollover or not because the Form 1099-R doesn't indicate whether the distribution is rollover eligible. For example, a distribution from a 401(k) would be rollover-eligible and would be reported identically on a Form 1099-R. TurboTax relies on you to only report rollovers that were actually made and were eligible to be made.
The IRS also receives the Form 5498 issued by your IRA custodian indicating whether you made regular or rollover contributions. In this case, the IRS recognized from the Form 5498 that you actually made a new contribution, not a rollover contribution, so they allowed the IRA deduction on Form 1040 line 32 or Form 1040A line 17, but disallowed the exclusion of this portion of the pension distribution from Form 1040 line 16b or Form 1040A line 12b.
If your state taxes this pension income, you'll likely need to amend your state tax return to make the correction there as well.
