The monster zoo effect (and counter) cancels if you enter your pocket dimension, leaving you with no reward when you finally empty it. No idea if this is working as intended, it might be. Also, if you open one monster zoo it activates all of them on the level (and allows you to view the others on your mini-map).
It has been quite a while since this was discussed, but I believe it is fully intended. If you leave the level, you forfeit the reward. And multiple zoos are just an unintended feature. They are not exactly bugs, but they were not intended. It all has to do with the way levels are generated.
The game also used to cancel zoos if you entered a shop. The current way you get "rewarded" for beating them without resorting to extended inventory or hopping floors to recover resources. Now if the next patch would buff reward quality and make zoo monsters incapable of going passive...
