The concern is a visible gasketed fastener
An exposed screw is part of a fastening-and-sealing detail, not just a hole to fill. Ask whether the finding concerns the washer, installation geometry, fastener compatibility or the material receiving the screw. A proposal to use a larger fastener should explain suitability for the actual roof rather than assume that bigger or tighter automatically restores a seal.
Notice next: Supply earlier screw-replacement invoices and ask for the specification behind the proposed replacement.