Plot hole: The Triforce of Wisdom is kept in Link's room up in a tower. It does seem logical to keep it with Hyrule's greatest hero to keep safe, but that's all you ever see protecting it. Hyrule is a large kingdom, and the Triforce of Wisdom is a vital part of keeping their community safe. Yet the only one protecting it is Link. And he's not with it 24/7. The room is not very secure either and is breached all the time by Ganon's forces. A kingdom like this would have knights to post all around the tower and be in Link's room when he's away. But nope, not here. (00:01:10)
Plot hole: Whenever Gretchin calls Mikey up to the stand to explain what he saw, he says that he had followed Spinelli and Randall to the wooden fence, where he Saw Randall on his knees in front of Spinelli, begging for forgiveness, then Mikey began running to the other side to stop Spinelli from pummeling Randall with the "rock" but didn't make it in time. We then later find out that Spinelli had actually rescued Ms. Finster's cat out of a tree and Randall hit himself with the rock out of spite. But it is impossible that Spinelli could have given up on hurting Randall, climbed up a tree, rescued a cat, climbed down, handed the cat back to Ms. Finster, gotten praise from Ms. Finster, then have Randall attempt to pick up a big rock, then get a smaller one and hit himself with it in under 3 seconds (the duration of how long Mikey ran before he heard Randall's scream).
Desertion of the Dinobots (1) - S2-E19
Plot hole: Perceptor discovers that the reason for their malfunctioning is because their Cybertonium has deteriorated after millions of years of being exposed to Earth's atmosphere. The key word here being 'millions'. This explains why the original Transformers who crash landed on Earth (4 million years ago) are affected, but newer characters like Perceptor, Powerglide, Hoist, etc. are affected despite the fact that they have only been on Earth recently.
The Powerpuff Girls Best Rainy Day Adventure Ever / Just Desserts - S2-E10
Plot hole: The children decided that they hated the Powerpuff girls in one day. Then how did they have supervillain costumes and a van? The mom said they had lots of time to prepare.
Sins of the Fathers Chapter 6: Framed - S3-E6
Plot hole: After Peter Parker is framed and arrested for selling government secrets to foreign organizations, he escapes police custody and goes home to retrieve his Spider-Man costume that was simply hanging in his dark room. If he was arrested for selling government secrets then surely the police would have searched his home and found his costume (as well as equipment) in the process. Since the police car was visible in front of his house, it seems very strange that police didn't search his home.
A Gummi By Any Other Name - S1-E9
Plot hole: The Changing Hat has the habit of transforming its wearer at the mere mention of a name (or even a species type, as seen before when Sunni accidentally transforms into an ogre). However, when Calla impersonates Igthorn and faces off against him, she loudly says the name "Toadwart" and doesn't transform.
Plot hole: When Lawquane spots the droids in the field, he identifies them instantly as commando droids. But as he had left the Republic Army shortly after the first battle on Geonosis (the one which started the war) and has lived as a farmer ever since, and since the commando droids are relatively new (see "Rookies"), how can he know what they are? With his lack of battlefield experience, he should simply call them battle droids.
The Kidney Stays in the Picture - S7-E16
Plot hole: It is explicitly stated in this episode that Hayley was conceived in 1996. While normal for shows without character aging to change birth years to benefit the plot, this move was premature. Hayley's permanent age is stated as 18, and this episode implies that in 2012 she would be much younger than this. The whole plot centres around her being legally able to drink in a bar, so this is a pretty big mistake.
Plot hole: Series 2, Episode 11, The Agenda (1). The Tripredacus Council explains that Ravage will be able to find Megatron and the others by tracing the transwarp wavefront back through time to its source. If he truly did follow it back to when it started he would have arrived moments after Optimus destroyed the alien weapon in "Other Voices: Part Two" which created it, yet he arrives considerably farther in the future.
Plot hole: When the DigiDestined return to the real world, Izzy states that only a few minutes have passed by despite the weeks that have elapsed in the DigiWorld. However, in an earlier episode, Tai returns to the real world for hours and upon his return to the DigiWorld, only a few weeks have passed by.
The Mutation Situation - S2-E1
Plot hole: The Krang ship carrying the shipment of mutigen is small, about a scout class ship. And it is seen flying past April and only a little bit above the top of the lower buildings in the city. The turtles have time to fight for a bit allowing the ship to get quite far away from April and her father. Yet Mikey accidentally causes all the canisters of mutigen to fall out of a hole in the floor and most are seen falling directly straight down towards the street, the ship being only about 5 to 8 stories above the ground. Yet somehow when it cuts to April seeing this, suddenly the sky is full of and raining canisters all over the city. And if cuts to her face even showing them raining down behind her. Which makes no sense because of how low the ship was, the canisters falling directly straight down in a tight cluster, and the ship having passed April a while back.
Worlds Collide: Part 3 - S3-E6
Plot hole: In their previous encounters with the Triceratons, the Turtles had to learn the hard way that the Triceratons breathe not oxygen but a combination of nitrogen and sulfur, which is detrimental to most Earth lifeforms, and thus had to wear special rebreathers. When the Turtles, Splinter, April and Casey enter Zanramon's throne room along with Traximus, none of them wear any breathing equipment to protect themselves from the hostile atmosphere.
Normal Boy/Birth of a Salesman - S1-E3
Plot hole: Throughout the show, many characters state that Jimmy was responsible for the meteor almost destroying Retroville in the episode "Normal Boy", however, how would anyone even know that? The meteor was put on course after being hit by some kitchen objects shot into space by Jimmy's orange juice machine. Neither Jimmy nor his parents or anyone saw the objects go into space, much less witness them causing the meteor head straight to earth, especially since the meteor wasn't detected until the next day.
Cigars of the Pharaoh: Part 2 - S1-E7
Plot hole: The doctor at the mental hospital reads the letter Doctor Finney wrote him. It read that it was Tintin who was insane and Doctor Sarcophagus who wasn't insane. However, although he totally bought it, he never even took into account that Doctor Sarcophagus was pant-less or the fact that he was dancing like an Egyptian guy, which would have been enough to prove that Sarcophagus was the insane one. (00:33:15 - 00:34:00)
The Aptitude Test / Oskar Gets a Job - S3-E9
Plot hole: Mr. Simmons asked that each student put their name on the test folders, but the folders already had names on them when he handed them out.