The List of Errors is a page which marks the series' certain notorious animation errors, even (though rare occasion) in the plot.
- In the beginning of the theme song, when Randy dressed as the Ninja is standing on the school, he has visibly black eyes instead of his normal blue eyes.
- During the hallway scene in which the characters are shown in the theme song, Morgan's hair and lips are blue, instead of their normal color of purple.
- There are many times where one or more characters in the background appear in two different places.
- One normal and constant error is whenever a hairstyle switches sides, like Theresa's hair streaks and Morgan's ponytail. This seems to have lessened in some recent episodes.
- A more obvious example of this is in "Night of the Living McFizzles", when Howard's zombie face keeps switching sides.
- During one scene in the Norrisville High Talent Show in "So U Think U Can Stank", Howard appears to be in two places at once.
- In the overview of "House of 1,000 Boogers" some of the characters can be seen twice.
- After admitting his secret identity because of McFist's device in "30 Seconds to Math", Randy's eyes are normal, when they were yellow earlier, as Howard walks through the crowd in a shot.
- In "Silent Punch, Deadly Punch", when Randy jumps out of the fake chimney, the chair next to him is empty. But in the next scene, Bash and "Santa" are sitting in it.
- In the same episode, Randy uses his old sword, but also uses Ninja Rage, which he learned after he got his new sword.
- In "Dawn of the Driscoll", when Randy and Viceroy first get in the car, Mrs. Driscoll is wearing her lab coat. However, when they reached Jerry's secret hideout, Mrs. Driscoll is wearing her skeleton costume again, in the same episode at the end when Randy and Howard look into Mrs. Driscoll's class room Randy is seen with his cow costume but in the next part the cow costume is gone
- In "Viva El Nomicon" when Randy is trying to open the Nomicon, Randy's mask can be seen with no lines on the lower part of it.
- At the beginning after Randy bumps into Bash the under of his eyes and the right tip of his teeth are a dark blue instead of a light blue.
- In "Monster Dump"'s beginning, when we see the back of all of the students, we see that Randy doesn't have his book bag with him. The camera moves to another shot, then goes back to the shot of the back of the students, where we see that Randy has his book bag with him this time.
- In "Evil Spirit Week", Howard is wearing his western outfit in the cowboy cafeteria, but when he gets on top of the vending machine, he's wearing his normal attire.
- In "Bash Johnson: 11th Grade Ninja", after the Sorcerer says he learned the Ninja's secret identity, McFist raises his right hand to his chin, showing his normal hand, not his robot arm.
- In "Hip Hopocalypse Now", Howard is wearing shades during the rap battle, and takes them off before he hands the microphone to Randy. But while Randy's rapping, Howard is dancing in the background with the shades back on again. A scene later, his shades are off again.
- Steve Riley is supposed to be a robot made by McFist to beat Norrisville High at chess in "Stanks Like Teen Spirit". But a human Steve Riley, along with other Flackville High students, keep appearing as a background character in various episodes.
- Throughout "The Ninja Identity" and "The Ninja Supremacy", Howard is wearing a costume with gray hair for the history report he and Randy worked together on. But when Randy pulls the Ninja Mask off of Howard, his normal hair and eyebrows are seen before they're back to gray in the next shot.
- Howard is wearing a girl disguise in "Enter the Nomicon", but in a shot where Randy and Howard's backs are seen while they watch Mac Antfee, Howard is wearing his usual outfit until the next shot.
- In the same episode, while Randy is firing the Ninja Air Fist, Randy completely disappears from the background for a millisecond.
- During the parade in "Bring Me the Head of Ranginald Bagel!", Theresa is twirling in front of Norrisville High's float while the marching band is surrounding it. In a later shot, the band is holding a Robo-Ape balloon while Theresa, dressed in her Halloween costume, is holding it with them.
- In "Randy Cunningham: 13th Century Ninja", Theresa and Bucky are stanked in the school right before the Sorcerer spots Julian, but later they are seen still with the tour group at McFist's factory.
- In "Shoot First, Ask Questions Laser", the destroyed Laser Bots disappear after the mobs point at Randy and Howard.
- In "Snow-Klahoma!", at one point, the Ninja has two scarves.
- In "When Howie Met Randy", when the Ninja of '05 first appears, his right hand glove is missing, , and in the next frame, the glove is on.
- In "The Fresh Principal of Norrisville High", after everyone has put on the helmets, Randy has no torso for a brief shot with him and Howard.
- In "Big Trouble in Little Norrisville" , when cloaked Julian got Randy's scarf, he has two fingers but when holding the scarf, his fingers turned three.
- Although this is probably just because episodes have separate plots, Randy finds the "freeing the chicken" step of the Ninja Air Fist hilarious in "Monster Drill", but is actually afraid of chickens in "McFear Factor".
- In "Swampy Seconds", Randy learns Catfish's name when he is captured, but without explanation he knows Catfish's last name is Booray later on while trying to save Howard.
- When Randy wakes up in "Ninjaception", Randy and Howard are apparently capable of touching a Chaos Pearl without getting corrupted by it, which they originally weren't able to do in "Julian's Birthday Surprise".