This is the CLASSIC reason for innocent spouse relief
Not to make light ... but you are the POSTER child
for innocent spouse relief.
What's happened here is the system has just captured it, as it always does when there was a joint return
, and they're dragging their feet on granting it (as they always do - even worse right now with resources being stretched) and getting it into the system.
A professional ... a CPA, even better a tax attorney, who has the special access for these issues is your best bet.
Based on what you've said here they'll be able, not only to get it granted and into the system, but get it granted effective the day you requested and get you a refund.
Sorry for no simple answer here, but the real-world answer is get some hep from a tax pro that has experience with ISR and this should go away relatively quickly.
Not sure where you are, but this is an example of of the kind of person you're looking for...
Let me know if you have questions...