WIP warehouse empty, parts stuck

We are seeing a problem where assemblies are being completed, but the warehouse location they are put into for wip is blank. We have the out bins set for all of the resource groups, but I am showing negative part quantities in the bins that parts are getting pulled from, with the opposite positive qty in no location. Somewhere the part needs to have a wip location written and it's not being written in the database. Then when you try to ship it, it says that there is not a valid WIP location. If I could move the parts into our bin location, they would drop off the list like they should because they've been shipped.