Unfortunately this happens to me fairly regularly, although usually with carnivores. I've mentioned it in other sections and so have other people. It seems to maybe be a fencing or elevation bug (where guests think either they're in the exhibit or the animals are out of the exhibit when they aren't) but unfortunately there isn't a fix as far as I know. If things start getting too crazy I do what you already mentioned, just close the zoo and make sure everyone clears out before reopening. :8