It sounds like you may have made an error reporting the form 1099-R that reported the conversion. After you entered the form 1099-R, you should see a screen that says What Did You Do With The Money from (name of broker)? You should choose the responses I moved the money to another retirement account and then I did a combination of rolling over, converting, or cashing out the money. On that same page you have an opportunity to enter the amount converted to a Roth IRA. Later on you answer the questions regarding nondeductible contributions to your IRA. I think you may have entered the amount converted to the ROTH IRA in the IRA contribution section, and that would bring the excess contributions issue into play. @TR571
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