At around 48min where Jack chases the three bears and Goldi, he takes his sword and swings it from right to left (from his point of view) but the bears and Goldi fly down the right side, not left, as it should've been.
At 36 minutes and 21 seconds in the movie, Kitty Softpaws is fighting with Puss over the map. Her name derives from the fact, which she later tells Perito, that she was declawed. At the 36:21 mark, you can see that she is using claws from what would be her thumbs to try to wrestle the map from Puss. This is the only instance and happens before she tells that she has no claws.
When moments from Puss's first eight lives are flashing before his eyes, a memory of Shrek 2 is shown before memories of the first Puss in Boots movie. While this matches the real-life release order, the first Puss in Boots movie is actually a prequel that takes place before any of the Shrek movies, making the chronological placement of the Shrek 2 memory incorrect in-universe. However, it was confirmed that Puss in Boots: The Last Wish was set after the main Shrek movies, making the flashback correct. This is known because of a memory of Puss' seventh death, where he is seen baking with Gingy.
The serpent sisters instantly switch places when the camera changes after one looks at the shrunken ship in a bottle.
Pinocchio sings he is a real boy, but his nose does not grow from the lie as it normally does.
When Puss in Boots is flattened by the bell, the bell tolls loudly. When the bell hit the ground it should not have made such a loud sound.
At the beginning of the movie after Puss wins against the giant, he is standing under the huge bell while the bright sun is casting a shadow of Puss on the floor. When the bell is hanging above Puss right before it falling down, a shadow of the bell should be seen too, but there is none.