Because it's the TSA? It's possible that both bottles fell out and broke and they only placed one in the plastic bag and the employee didn't want to officially declare that the TSA had gone through bag by placing the card in the luggage...

The zipper-getting-snagged scenario would have been after the bag left TSA and was put into WN's hands. It's possible the other bottle fell out someplace in a cart or conveyor belt and couldn't be matched with the bag.

Of course this situation could have been an improper opening of baggage and theft, but man, that's pretty hard up if TSA or WN employees are so desperate to steal a bottle or two of wine.