For the form with 0 in box 9(a), you need to leave that entry blank, as that will mean it is zero. The issuer of the form should not have put zero in that entry.
If box 2(a) is zero, it will also be treated as being blank and the program will default to indicate that the taxable amount is not determined. In order to determine if the distribution is taxable, you need to answer the questions in TurboTax that you will be asked after you made the form 1099-R entry.
Also, the code(s) in box 7 will be used to determine if the distribution is taxable.
Often, the issuer of the form 1099-R will leave box 2(a) blank or enter a zero, but the amount is actually taxable. That is why TurboTax does not accept a blank or zero entry as necessarily meaning the distribution is not taxable.
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