Be sure that you only entered the Form 1099-R to report the direct rollover from one IRA to the other IRA. This should not have also been entered as an IRA contribution because that could have triggered the Form 5329.
Go back to Deductions and Credits > Retirement and Investments > Traditional and Roth IRA Contributions and click Update to be sure there are not IRA contributions noted in that section representing the direct rollover.
If nothing is found in the contributions section, then try deleting the Form 5329. If there is still an entry in your return triggering the form, then it may not remain deleted or an error condition could be created.
@scobb01
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