The wrecked ship in the swamp is not level, yet all the levels that take place on it are on the level.
When the player goes to Kong Kollege, the outside environment appears as if they were at Gangplank Galleon, inconsistent with the actual environment of other worlds of Crocodile Isle.
Klubba's Kiosk first appears in the game's second world Crocodile Cauldron, but the environment upon visiting appears to be taking place in the third world Krem Quay, even before going to that world.
The purpose of the level Lava Lagoon is for the Kongs to cause Clapper to turn the lava into swimmable water in order to progress. In reality, when lava cools, it becomes an extrusive igneous rock depending on the process.
It is not possible for Diddy Kong and Dixie to breathe underwater while scuba diving without oxygen tanks as they are mammals. If Diddy Kong and Dixie Kong tried this in real life, they would both drown.
At Wrinkly Kongs school, you can see 3 incorrect answers on the blackboard. 9 divided by 3 does not equal 6, the correct answer is 3. 8 times 1 doesn't equal 9, the correct answer is 8. 4 plus 2 does not equal 5, the correct answer is 6. It's unknown if Wrinkly Kong or her Kremlings wrote the 3 wrong answers on the blackboard.
In the level Hornet Hole, the wasp enemies would not be able to produce honey as that's part of the honeybees job, it's possible that the hornets have invaded the honeybee hive and the honeybees would've likely attacked the hornets or wasps who invaded their hive. But the bees are seen sitting in the honeycomb background watching and doing nothing. Also the level Hornet Hole is incorrect as it depicts a honeybee hive. It should've been called Honey Hole instead.
The "lava" In the level Lava Lagoon is actually steaming hot water that is orange, but turns blue when Diddy Kong or Dixie Kong jump on Clapper that causes him to blow and cool down the water to make it swimmable in order to progress - which will re-heat after a certain period of time should the Kongs be fast enough to swim and escape out of it.
In Donkey Kong Country (1994), Rambi would pant while waiting for one of the Kongs to hop on his back and ride him. In Diddy's Kong-Quest, he pants but, there is no panting sound at all.
Krow, the boss of Gangplank Galleon in his namesake boss level Krow's Nest (and later as the boss of Gloomy Gulch in his ghost form as a rematch in Kreepy Krow) is depicted picking up eggs from the nest in the first boss battle he appears in and is referred to as a male. Males do not lay eggs, females do.