"Since I recharacterized to a Roth, the contribution was no longer tax deductible so I paid income tax on the amount that was recharacterized."
The contribution was never deductible to begin with, so you aren't paying any more tax.
A code-R Form 1099-R must always have $0 in box 2a and, when entered, TurboTax will never complain about that.
The message that you received suggests that $0 was entered in box 2a of a Form 1099-R that has code 1, 2 or 7 in box 7 with the IRA/SEP/SIMPLE box marked. The only time you are permitted to enter $0 on TurboTax's form in place of the amount reported in box 2a of such a Form 1099-R provided by the payer is if the distribution is nontaxable because it is a return of excess contribution after the due date of the tax return for the year for which the contribution was made, which requires explanation to the IRS.
