It doesn't sound anything like stealing. They offered you a gift, you made a polite refusal, they insisted that it would make them happy for you to take the gift, and you accepted when it became obvious that it would be ungracious to refuse.

I doubt the staff is allowed to take wine home. I think it was just their little joke to make you smile.

Drink in good health.

They may have a policy of occasionally gifting extra wine to make good customers happy, or they may feel a need to gift the extra bottle once in a while for fear that otherwise they might be under-catered on future trips and run into trouble. Perhaps you were the only WBC customer on that trip who seemed to appreciate the wine, but they know that usually there are lots of wine drinkers on that trip. Sound reasonable? You know how in academia if you don't use an entire grant one year, the next year then your grant will be reduced? Maybe they're worried about something like that happening.