Yup, running into pretty much the same bugs here too, currently have played about 4 Square Map Sandbox games, these are the bugs I encounter in every game:
1. The Dunks and Kronos willf freeze after sometime if eating sharks. I hear Mosos also do the same. This one's a real killer, hope Frontier addresses this one first. One cheap workaround for now is not to place any shark feeders, and I guess no Mososaurus.
2. The lagoon platform rocks and viewing domes get all crazy, with the cylinder bases of the platforms landing on top of the platforms and the viewing domes floating, all this possibly after a save? I noticed in another game the viewing dome did not float back up when I hadn't placed lagoon platforms. This one's real ugly lol. One workaround is not to make any Northos or huge Turtles for now.
3. Some species, especially Torosaurus, will come out of a hatcher halfway underneath the ground. But quickly resurface to normal, this one's not a killer like the other 2.
4. As for the medical bug, I have seen some weird glitches here and there but nothing too nasty.
5. The biggest bug of all tho, thankfully it does not happen everytime, is a Mososaurus getting stuck in a hatcher. This one will kill your game, pray you have a saved file before this actually happens, otherwise you'll end up with a dead dino skull on your screen and a dead undecaying Moso somewhere.
Besides that, game is ok, when I get the must be transported into same aviary bug with a flying dino, I either just reawaken it, or if it's really stuck, I'll transport somewhere outside the aviary and re tranquilize it and have it transported back...
Worst bugs are 5, 1 and 2 by far.