Yes, you are right, there are different problems with animals getting boxed, and probably different root causes. Probably those involving "physics glitches" that trigger the boxing inside the habitat due to some terrain element (I've had those as well, and animals escaping that way too). But even in a perfect habitat, an animal can get boxed if you displace or add a new element in that habitat (which I can understand). And finally, and that's the problem I was describing, animals get boxed randomly when I work on the opposite side of the park even though they never get boxed if I just watch them for a while.
Totally agree with your assessment of why the issue tracker is problematic, but to be fair that's a human-wide problem. Ask doctors, help desk workers, etc. Most times people give you irrelevant information, sometimes wrong information as well, so a clear diagnostic is very difficult to make. I think the most overlooked part of the issue tracker by users is the "steps to replicate" part. If a dev cannot replicate the issue for themselves, they cannot solve the issue - period. There should be a clear notice in red, how to fill in that area and what is the kind of info to be filled in to actually help the devs with their job.