After you file

NONE of the stimulus payments are taxable ... none at all.   What may have confused you is the way the program interview is set up ... the program gave you all the credit you are eligible for into the refund then when you finally tell the program how much credit you got in advance it reduces the refund by the same amount since you could not have the credit twice.  The result in the Refund-O-Meter looks like the stimulus payments were taxed but they were not.