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The taxpayer filed elsewhere.
This could be due to error or identity theft. If the taxpayer believes this is identity theft then they should file Form 14039.
The taxpayer's information is entered incorrectly and the IRS system thinks it is a different person (double-check the SSN, name, and birthday).
The taxpayer received a quote somewhere else, and they filed the return without their consent.
You are trying to file an amended return for a taxpayer you did not file the original federal return for, but forgot to check the e-file amendment box at the top of the 1040-X and the software is trying to send the original return.
Possible Resolutions:
If the taxpayer's information is entered incorrectly, correct the taxpayer's information and resubmit.
If the taxpayer did not file elsewhere, have them paper file and complete Form 14039.
If e-filing an amendment for someone you didn’t do the original return for, mark the e-file box at the top of Form 1040-X.