Happened once to me when I made a payment to my WF CC in branch. The returned MO was a copy of deposit image but not the normal returned copy from WU. Asked bank account manager and she had filed an escalation to WFCC Credit Card Executive Office.

The first response said "Yes we have completed the research and seems like Kroger might have made errors when they issued you the check. I have attached the copy of the check for you to take it to Kroger. It was returned because its flagged “refer to maker”. "

I requested further review and the 2nd response resolved the problem as "It seems like there were some other encoding errors. They are working on it... Once this is resolved, your payment will be backdated to the original date. "

And as she said, the money eventually appeared in my account two weeks later with original payment date.