Employer missed spouses short term disability payments and is asking for money back from makeup payments. - My spouse was out of work for about 2 months on short term disability over the summer. During that time her employer didn't pay her for an entire month. This was after the waiting period ended. Later after looking at bank deposits we communicated with the disability insurance company and they made what appeared to be makeup payments. Now her employer is telling her that they overpaid and we need to pay them back 1000.00+.
It seems that the makeup payments worked out to the correct amount to cover the 4 weeks previously missed. How do we determine what if anything is owed back to the employer?

Edit 1: My spouses short term disability insurance is provided by her employer.
When she was out, she recieved no payments directly from an insurance company, only from her employer.
She recieved pay for the first two pay periods after her short term disability started, then no pay for two pay periods, then some pay again. Also worth noting, we contacted the insurance company when we saw a gap in payment.