After you file

We did that. However, let's say, the original refund for MFJ was $1000.
On my side, the amended return to MFS gives me a refund of $300, 1040X shows I owe $700 back now. Ok.
On my wife's side, her amended return to MFS gives her a refund of $300, 1040X shows she owes $700 back now. It does not make sense. Should she put $0 on line 18 of the1040X?
Thank you.