More than likely the client went to an IRS portal to apply for stimulus benefits rather than just letting them arrive. In doing so, they in effect filed a mini return and so when filing the regular return received error messages that the return was already filed.
This happened twice to me this year. Never before in the past. First time I was on the phone with the IRS for days and filed a Form 14039 concerning identity theft. Second time I just had the client sign the returns and I mailed them for her. I wrote the rejection codes at the top of the return