Issue against a work order, every time
If a part can leave the store without a job number, you cannot later ask which car it went into. Make the work order the only door out of the store.
Treat returns as a transaction
A wrong-size filter put back on the shelf without a record makes stock counts drift. A return should be recorded the same way an issue is.
Compare issued parts with invoiced parts
Each week, look for jobs where parts issued do not match parts invoiced. The gap is where money is leaving.