I started having some of these issues too now, with my lemurs. Only 2 escapes over like 10 hours of play, but both were pretty random and it's not the enclosure...that's fine and has been for like 40 game years prior to this update.
I'm also getting a lot more frequent "auto-boxing" of all of my critters than I was before the 1.1 update. It seems I can't do any construction anywhere in my zoo without 2 to 3 habitats having a handful of animals boxed. My current zoo is nothing but primates and apes (plus a red panda hab), so they are all climbers....no animals in this zoo aren't though.