H1 Taxes Refunding

Has anyone had any experience with the  H1 taxes being refunded for an employee for no apparent reason, they are not near a wage limit, etc. for the year and it should be calculating normally, however it is trying to refund the full amount that has been paid thus far this year. The only thing on the vertex before and after report indicates that it is calculating a negative amount....Any thoughts or things that we should look at? We are on vertex 2.9.10

It only appears to be happening on interim payments.