Its number one, or a genuine mistake. There is no economic incentive to short a few pills because the computer which registers supply would automatically order new pills because it would think it has sold out. When you look on shelf or bin, there would be a surplus left over and someone would notice. Not veryone who works there will be crooked.
Pharmacy employees who are addicted, or in street sales, will break pills so they get "tossed" into throwout bin, but they retain a portion of the pill. The portion they steal is "dust" in a bin bottom for purposes of inventory and FDA issues.
Additionally, the antibiotic pill has no street value and is needed to be taken in a complete cycle, leading me to believe it is a mistake.