Last night I noticed the same thing that Svaca33 reported. I captured a city with a brewery but still had it in the build list for the cities I had founded. I didn't try building a second one so I don't know what the behavior would have been had a tried.
I have a related game mechanics question - if I get rid of the brewery after I've built a pub in each each of my cities, do I get to keep them or do they go away? In other words, am I required to maintain the 'mother' building to keep its 'offspring' buildings?