Vicky is seen driving the Striker Z from Engine Blocked. The reason why it looks beaten up in this episode because close to the end of Engine Blocked, the Striker Z got wrecked up after it fell off a cliff and crushed by a crusher in a junkyard.
Space Jam - After Jimmy tells Cosmo he isn't real Cosmo replies "If I weren't real could I do this? Or this?" This quote is the exact same words Bugs Bunny says to Michael Jordan when Jordan tells Bugs Bunny he isn't real.
The Simpsons - When Timmy appears in Jimmy's lab he notices that he is now "bulgy." This is a reference to the classic Treehouse of Horror VI short Homer3 where Homer says the same thing when he becomes 3D.
Although this special premiered in 2004, it was produced in 2003 according to the credits.
As noted in this episode, Hanna-Barbera exists in The Fairly OddParents universe even though in Channel Chasers, HB's shows are parodied.
When Jimmy takes Cosmo's crown to make an electromagnetic field, a shot of the invention has Cosmo in the frame wearing a crown.
When Timmy was in A.J. lab, a picture of A.J. and Albert Einstein was seen but this picture is non-canon. As A.J. born in 1992 and Albert Einstein died in 1955, A.J. could not have participated in this picture with Albert Einstein since Einstein died before A.J. was born.
Timmy's wish defines Jimmy's lab as the greatest one in the universe, implying that Retroville and Dimmsdale are of the same universe, or maybe Cosmo and Wanda accidentally sent him to another universe. However, later in the special Timmy claims that he loves "this" universe, implying that the two are separate universes. Timmy later asks Cindy if she has a camera capable of sending a picture to a parallel universe which is arguably the best definition of the two towns. Jimmy says "I not familiar with how you greet people in this Dimension.". This might not be a goof because Timmy says "I wish I was in the greatest lab in the universe." but he isn't specific on which universe.
Jimmy pours out the water in the fishbowl, but when he looks under the bed, it is back in the fishbowl.
Mr. Crocker unplugged the Big Wand and yet Fairy World did not fall into the Giant Bucket of Acid World. However, Mr. Crocker might have been the one that was keeping Fairy World levitating as he was using a weapon that allowed his wishes to be granted.
Timmy feels perfectly fine when he takes off the helmet, unlike when Jimmy was still a little dumb after he drained his brain in "Normal Boy".
When Jimmy turns Mr. Crocker back to normal with Jorgan's wand, Mr. Crocker is seen wearing his normal clothes, but when Jorgan is seen getting ready to "shred" Mr. Crocker he is back in his battle suit.
When Jimmy takes Cosmo's crown to create the electromagnet, Cosmo is still seen with his crown on his head.
In the first shot of the inside of the Science Fair, Mr. Crocker is on the stage, but when Principal Waxelplax explains what happened to Mr. Crocker, he is on the floor.
Timmy wishes for both Jimmy and Timmy to be in their hometowns. This creates two or three errors.
1. The two should not have been able to interact as Cosmo and Wanda should have just poofed Jimmy into Retroville and Timmy into Dimmsdale.
2. The portal that Jimmy came from and Timmy was going to was Fairy World, not Dimmsdale.
3. Depending on one's definition of a hometown, it is possible that Jimmy should have been sent to his birth town, which is most likely not Retroville because in "Jimmy Neutron: Boy Genius", Cindy reveals that Jimmy Neutron moved to Retroville.
When Jimmy and Timmy shake hands, the two hand animations don't overlap like an actual handshake should.
When Mr. Crocker slams open Timmy's door, the door slams to the continuation of the same wall that the door is on. However, when Mr. Crocker shows that he has the Teleporting Game Buddy, the door is on a perpendicular wall.
Also how did Crocker break into Timmy's house without meeting Mr. and/or Mrs. Turner, when he should've broken in through the window?
Probably he disguised himself, or just he knew that Timmy's parents are nitwits so he used an excuse to get to Timmy's room.
Retroville shows up on the Game Buddy before Jimmy presses any buttons.
When Mr. Crocker shows that he has the Teleporting Game Buddy, Retroville is not shown on the Game Buddy's screen.
In the scene where Carl and Sheen meet Timmy, Goddard is shown in the background. Goddard's ear is not leaking. However, when Goddard is shown to start feeling the effects of the Decimator game, his ear is leaking again.
When Timmy is looking through Jimmy's inventions in his lab he finds the shrink ray and tests it out as he does it the remote shrinks too despite it not shrinking with its test subject in numerous The Adventures Jimmy Neutron: Boy Genius episodes
Cindy's arms appear to clip through her shirt various times throughout the episode, notably whenever she goes to kiss Timmy