Zoo Tycoon 2 has many various known glitches. As of now, only one patch has been released to fix these problems.
- Sometimes guests will flee from an animal which is in its exhibit.
- On occasion, guests may teleport into exhibits at random.
- Guests occasionally fall through elevated paths.
- Dwarf Sicilian Elephants who have been cured of the Pink Elephants Disease may still appear pink.
- Zookeepers and Guests may randomly appear to be headless or bodiless.
- Animals may appear to walk on deep water.
- Animals may appear transparent.
- In Challenge Mode, the animal sickness challenge may be listed as failed even if the challenge was not accepted. The message says that the players '%' has become sick.
- At times, if you window the game and then unwindow it, the letters will appear thin and pixelated (as if playing in low resolution), instead of the regular bold lettering.
- One photo challenge requires the player to take a picture of a guest talking to a hand puppet. Unfortunately, Blue Fang never added the behavior of the guests talking to the hand puppet. As a result, if the player accepts the challenge, they will have to quit without saving or start over entirely due to the lack of a time limit on the challenge.
- On some installs, the game will crash after loading three freeform or challenge maps. This bug has only been observed in Zoo Tycoon 2: Ultimate Collection.
- In the original, unpatched Zoo Tycoon 2, the game would sometimes crash when the map is left without any animals for a short amount of time.
- An issue with older versions of the biomeshell causes the Dino Rampage Center to disappear.