Here's a question... when did the cloning process start? What little information we have doesn't provide a date. Cloning was not part of its original mission so we shouldn't assume they started cloning Gary's right after the doors sealed. Either the terminal in the entry in the Citadel about the vault's purpose was a lie or the Cloning process started long after the vault first closed.
They ate them.
Prove its the same clones oh and prove the log wasn't written a year ago.
Ah but look at how it strings together with a couple other vaults.
Vault 87 was retooled for researching FEV
Vault 108 ended up producing clones
Vault 92 tried to use "subliminal suggestion." to program people.
Taken together you have an army of genetically enhanced super soldiers you can grow in lab and program to your heart's content. Of course each experiment was a partial failure