HSA - Vendor Overcharged and refund was sent back to HSA - Now it's a contribution?

At the end of 2017 there was an HSA paid expense that was overcharged by the hospital.  They couldn't issue a credit back to the HSA card, so they issued a check.

In 2018 the check was deposited and the funds (shown on 2018 form 5498-SA) were redeposited into the HSA account.

This is now showing up as a contribution on the 2018 form 5498-SA.   

If it gets entered as a contribution on the 2018 tax return is gives a higher refund, which isn't felt to be fair since it's not truly and additional contribution, but a reimbursement from the prior year's expenses.

How should this be handled?