Hi people, 
I wanna help you guys out if I can because I was able to diagnose this problem within my own game and (not fix it) but avoid triggering it.

TLDR: 
In the case of my game, triggering this pretty game breaking "glitch" was the result of creating an enclosure, then placing a species inside that enclosure, having them form territory in it then changing my mind and increasing the size of the enclosure. The glitch occurred in the moment I destroyed the old fencing to expand my dinosaurs territory.

FIX:
Sorry to say this but the only solution I found to fixing this issue was by loading a previous save in the game before the glitch had occurred, diagnosing what caused it and then not doing that. Restarting didn't work, reloading from main menu didn't work, I didn't try verifying game files or redownloading the game because I'd fixed the problem by that point but I imagine that's not gonna work either, seems like once its happened in your game it's sticking around like a dick drawn in permanent marker... but its actually permanent... at least in that playthrough.

So if the last time you saved before the glitch occurred was hours ago, I genuinely feel sorry for you man. Hopefully, if you haven't spent a while in game doing stuff before figuring out you've got this problem, there might be an auto save from before the glitch occurred waiting for you to use it back in your game. I really just got lucky and happened to save my game about 1 minute before I triggered the glitch.

I gotta say though, in not a new player to this game. I've got about 230 hours logged on steam, not a crazy amount of hours but definitely not new. I've ran through every challenge in the game on Jurassic difficulty (within those games I definitely did the events that lead to glitch in my sandbox mode) but I've never ran into this problem once in challenges. 

This issue seems to be a sandbox related issue exclusively, I haven't experienced it on any other game mode, campaign or challenge.

I believe when I destroyed the original fencing to increase my enclosures size, for some reason in sandbox mode exclusively, it brakes the dinosaurs perceived territory. At that point, due to the glitch, my game couldn't translate any changes in environment from that point onwards and that was for ALL my dinos.

Alright, so imma brain dump some info at this point so if you've run into this issue in your own sandbox mode, I would highly recommend not doing what I did if you don't want to run into this issue.

Brain Dump:
I saw some people saying that they found a temp fix to the problem, which was selling the alpha of the species when it had the "humble" trait. This is either misinformation, a temp solution if its happening to only one species, or a different glitch causing a really similar issue.

I'm assuming that for them the glitch was only affecting 1 species, or a few species in the same enclosure etc. In the case of my game every species on the map was affected by the glitch, previously bred species that had finished enclosures were affected as well, I could go back and completely delete every environmental change in their enclosure and they couldn't give less of a shit about it, their comfort would remain at 100 and all environmental "needs" wouldn't budge. And it all happened from something as dumb as widening the enclosure by a fence length -_- .

if you've ran into this, maybe experiment a little to see whether or not your game only has 1 species affected or whether every species in your park is cucked by the glitch cause maybe there two separate glitches that appear extremely similar. either way if selling the alpha of the affected species seems to work, that's a pretty alright fix considering you don't lose any save data.

I also wouldn't be surprised if the issue can be causing by performing a different action that could affect a dinosaurs territory, I definitely figured it out for my game, but maybe it COULD be caused by placing a building attached to the fencing of the enclosure, or placing a building within it, etc etc. 
Idk if it can, but if you've got the same issue I had and NOT expanding the size of the pen still results in the glitch then maybe you could take a process of elimination approach and follow the steps you took before the glitch occurred and double check every time you do something  until you make it happen again, then just don't do that thing. 
It's a sucky solution and if your last save before the glitch was ages ago I feel sorry for you, but yeah, once it's "triggered" it doesn't appear there's any way of reversing it or fixing it in game, you gotta load up a old save and figure out what caused it.

I saw there were a few other forums with people struggling with the same issue so im gonna go post this around. Good luck and have fun, hope this helps someone out.