I would start by verifying from the production batch record whether the correct number of sample bottles was pulled/transferred to QC Stability. If it was a typo on the QC Stability end, the BPR would indicate the actual # of sample bottles pulled for stability.
Conduct interviews with all personnel with access to the storage chamber to determine who might have accessed the material and if they had relocated it without proper documentation. That would include Facilities personnel to see if they moved the sample bottles as part of calibration/maintenance activities.
Investigate whether the QC analytical department pulled samples for additional testing [yes it is pretty far from lot release, but it is worth checking] without documenting in the inventory system. Testing documentation would confirm that samples were pulled. The testing documentation should reference a unique identifier to one of the missing sample bottles.
Perform the 100% inventory verification to check if it was moved to another storage unit but not documented.
A formal investigation should be initiated to identify the root cause of the inventory discrepancy; any gaps in the chain of custody process, sample distribution/receiving instructions or whether it was human error, etc. A process improvement should be able to be identified to prevent recurrence.