Why would an uplanned WO issue appear in the item ledger and not on the parts list?

We are experiencing intermittent problems with work order issue transactions being recorded in the item ledger but not on the parts list.  The problem occurs when we are swapping out one part on a work order for another but I cannot replicate the issue on demand.  We have seen it occur both when someone goes directly into the work order issue screen and issues the new material and when someone has updated the parts list with the new item and then goes in and issues it.  The problem never seems to occur when issuing a standard BOM part.  Wondering if