If you received a distribution for the full amount of your required RMD, when you enter your 1099-R in TurboTax, you are asked if 'all or part of this distribution is RMD'.
If you chose 'Part' try choosing 'All' and then indicate the amount of your RMD on the next screen to remove the penalty.
If you're using TurboTax Online, you could clear your Cache and Cookies before making the changes.
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