Yes, if it was just a name/SSN mismatch should cause a R0000-500-01 reject code.
"it does not have a return listed this year, does that rule it out?"
I am not sure how quickly the transcripts are updated at this point, so, as you say, this may not mean anything yet.
I would start the tax identity theft process. If you can speak to a person at the IRS, you might ask them to confirm that a return was actually filed. If no, then the question is why your initial attempt was rejected with a IND-664-02.
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