It seems that you have possibly entered both a Traditional IRA contribution and a Roth IRA contribution as part of your return. You should enter the Traditional IRA contribution, because you did contribute to that account. However, converting the Traditional IRA to a Roth IRA is not considered to be a Roth IRA contribution and should not be entered as part of your return in the contributions section.
Entering the Form 1099-R reporting the distribution from the Traditional IRA and answering the question about converting the money to a Roth IRA is all you do with regard to the Roth. There should not be any Roth excess penalty imposed.
Take a look at the following TurboTax help article for the steps used to report a backdoor Roth IRA conversion and make sure that this is all that you have entered:
How do I enter a backdoor Roth IRA conversion?
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