Your 1099-R 2020 for a return of the 2019 excess contribution and earnings should have the contribution plus earnings in box 1 $6,005.09 and in box 2a the earnings $5.09 with code 1P and box IRA/SEP/SIMPLE checked. This 1099-R need to be added to your 2019 amended return.
If you did not receive such 1099-R then you might want to contact Vanguard for the correct 1099-R because if you enter things different than what it is reported to the IRS then it can cause confusion.
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