for your first issue, it sounds to me like the document actually existed sometime but it was deleted without deleting its references from management console. So even though the document doesn't exist anymore it still appears on the server. So it comes the second issue. It can be that the document had X number of document CALs assigned, but since it was deleted from server but not from management console, the reference continues to be there (including those "ghost" assigned CALS).
The workaround I can think of is creating a "dummy" file with the same filename and then deleting it first from Management Console and then deleting from Windows. It would be a good practice to do this everytime you need to delete a QlikView File,