Receiving a message that your income is too high to deduct your contribution is nothing to worry about as long as you indicated that you wanted to make the contribution non-deductible. It needs to be non-deductible so that when it is converted to the Roth IRA there is no tax consequence.
If you had indicated that you wanted to deduct it anyway, then you would have seen messages about it being an 'excess contribution' that needed to be withdrawn by the due date of the return.
Since your numbers changed after you went through it again, it sounds like everything is squared away now.
@Locos1969
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