In my experience it could point to the fact that Document CALs were still tied to a model that was deleted. The easy fix would be to make a copy of an existing model under access point e.g. and rename it to the deleted model, then on QVMC select Socuments>>User Documents>>The deleted model>>Document CALs
1) delete the licenses
2) change "Number of CALs" to zero
3) select apply
4) delete the old model
The "Document CALs not allocated on server" number should now include the 3 lost CALs.
If you can't recall the name of the deleted models, then you might have to go this route: