When Mr. Bleacher asks Willy by the stairs what he meant when he comments about Mrs. Scribbit being "in love," Willy is seen wearing his coat. The scene then jumps to Willy holding his coat instead, and there was no time for him to have taken it off.
Upon exiting the Church, the Wonka crew tell Noodle they located her mother working and living in a library; However, it would be physically impossible for anyone but Wily and Noodle to know her name was "Dorothy Smith," for after they found this information they were caught by the cartel and locked in the chocolate chamber. There is no way the rest of the crew know this information.
When Noodle and Wonka are flying, they reach an antenna at the top of a building. They seem to get farther from each other, but after a cut jump, see can see them hand in hand.
When the Chocolate Cartel confront Wonka in his shop, the first shot of the three of them is from behind, and Prodnose has his umbrella slung over his left arm. In the following shot of them from the front, it is slung over his right arm.
Willy's wet hair on his face after his head is shoved into the water fountain's cold water.
Wonka and the Oompa Loompa discuss Wonka's theft of four cocoa beans, when in fact what he stole were four cocoa pods, each of which contains many cocoa beans.
At one point, Wonka has to milk the giraffe, Abigail, yet no infant giraffe is shown or mentioned. The giraffe would not be in milk without a young giraffe nursing it.
Flamingoes are tropical birds but are seen in the snow. Any zoo would have to keep them in a heated aviary for survival in winter.
In the first musical number with the chocolatiers, the chocolatiers are seen starting to float. As they do, Prodnose loses his toupee but in subsequent scenes in this number as he is floating it is still in place. This is because, as they start to float, one of the bystanders can been seeing throwing it back to Prodnose. He puts it back on between shots, which is why it is on backwards in the later shots.
While Willy Wonka and Noodle were trapped in the chocolate chamber and about to drown Noodle yelled out "Wally" instead of Willy. The caption for this scene said Willy.
With 11 minutes left in the movie, he breaks the chocolate bar his mother made one to many times. Instead of the six pieces he cracks it a extra time making a 7th.
After the Oompa Loompa saves Wonka and Noodle from drown in chocolate, Noodle asks who saved them and Wonka replies "I don't know" but his mouth is open while looking around in awe.
Wonka is touted as a prequel to Willy Wonka and the Chocolate Factory but the three chocolatiers, Slugworth, Prodnose and Fickelgruber, who are arrested at the end of Wonka are actually the rivals of the later Willy Wonka and the reason he closed his factory down, due to spies, and brought the Oompa Loompas on board.