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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.
- This is caused by an error in the coding with either the head or the body, as the head and the body files for Guests and Zookeepers are in different locations.
- Animals may appear to walk on deep water.
- Animals that cannot swim may also walk on deep water and even cross them safely as on land or shallow 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.
- Sometimes, animals will become very hungry even if the correct food is placed for them.
- There is bug present in several campaigns that may cause your money to appear to underflow into debt, doubling every time you buy or sell any item or receive a donation. Trees being placed through the biome auto-placement sometimes returns your money to normal, but manually buying things and receiving donations will cause the glitch to reoccur. Your true balance can still be seen at the gate. Restarting your game completely may fix the problem.
- One photo challenge requires the player to take a picture of a guest talking to a hand puppet. However, 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. This has since been patched.
- Sometimes, when you load a zoo that you had already worked on, it may appear glitched. Things may be missing or the zoo map may include objects, (trees, plants, rocks), that it normally shouldn't. There is no known solution for this.
- In Campaign Mode, sometimes when a challenge or task is completed to the game that task isn't done, resulting in a failed scenario.
- Sometimes, if you have too many downloads, the game sometimes would crash or the computer will shut downs by itself/unexpected shutdown.
- An issue with older versions of the biomeshell causes the Dino Rampage Center to disappear.