I wonder how large/complex this zoo is. I've noticed in my zoos when they get very large and complex strange things begin to happen. Many of these events are simple like guest getting stuck out on an open path and random habitat alerts. Not saying this is your issue but the true game bugs occur more frequently in those large and complex zoos.
I do like bigger zoos, but this cropped up fairly early in the process. The affected habitat is within a larger building I created to house the "rainforest" habitats and exhibits within a taiga biome zoo. I've noticed that when a zoo is going to be buggy, the random issues with animals walking through glass, escape alarms when the animals are still in their enclosures, and weird staff issues can start to occur when the zoo only has a couple of work zones and not all that many habitats.
The thing that is really odd about this situation is this particular tapir had a penchant for walking across the glass barrier of his habitat, triggering an alarm, then walking back in. He was inside the enclosure when he died, and I don't recall an alert right before, but it's possible he walked through, then walked back in and died while the alert was still active or something. I should have released him or something when it first became clear he was such a "troublemaker," but he sired nice babies.
People have mentioned a desire for animal personalities in the game. I've always thought it sounded like a fun idea, but maybe we should be careful what we wish for. Sounds like "escape artist" animals already pop up randomly.
Right after he died, a vet came to remove him but got stuck inside the habitat, right by the animal's shelter (where the tapir died). The doorways were more than wide enough for staff to get through, and the area was traversible. He just stood there getting angry. Finally I fired him. He stuck around, but left when I deleted the habitat gate then re-made it.
I re-did the call vet alarm at this point, and that's when a different vet showed up and tried to get into the habitat by walking off the path and standing in the landscaping right outside the enclosure glass, nowhere near the habitat gate (which was also very close to the vet clinic). Nothing I have done has persuaded him to budge. It's like he has no pathing now, but deleting the path, deleting and re-doing the habitat gate, moving the habitat gate to be in front of him, deleting the barrier, placing a path under him etc. has had an effect. Not even deleting the entire habitat does anything.
It's actually kind of funny, if frustrating.