I am slightly puzzled because, if you knew from the beginning that filing jointly had higher taxes, then you should have questioned the result when amending from separate to joint resulted in an additional refund. You may not have correctly accounted for both spouses’ payments and refunds when trying to amend from MFS to joint.
Your transcript from the IRS website may show the adjustments that the IRS made to your amended joint tax return. I haven’t tried to use the transcripts for this purpose, but it would be worth looking at.
https://www.irs.gov/individuals/get-transcript
It sounds like you actually owed additional taxes on the joint return but failed to account for the original refund, so it looked like you were due an additional refund instead of owing a payment. The $2000 you owed represents a repayment of the $754 refund you shouldn’t have gotten plus $1300 in additional tax, possible from the loss of the UC exclusion.
If you had asked back in 2020, there might’ve been a way to fix the Roth problem without needing to change to a joint return. Unfortunately, it is now too late to amend a joint return back to separate.
