
Independent Dependents - S1-E7
Plot hole: When Helen goes into the air ducts, she simply removes the grates. They would not be loose like that, they would be firmly attached. When the team enters the basement they go through an ordinary door by picking an ordinary lock. A very high security installation like Axe Industries would not have such an insecure entry, even into the basement.

Plot hole: While Mundy is trying to disarm the briefcase bomb in the study, his time-sensitive work is interrupted no less than 6 times by people barging in from the party out front. The plot device adds comic relief, but there's no earthly reason why he couldn't have locked or barricaded the door in the first place. (00:36:00)

New York City Serenade - S3-E12
Plot hole: When talking to Hook about the photos, Emma states he could have photoshopped them to make it look like she and Henry were in Storybrooke, however she had taken them directly from Henry's camera and had them developed. So Hook had no way to photoshop the pictures from inside the camera. (00:27:00)

Plot hole: Guards at a security checkpoint attack Varrick and Bolin, because a wanted poster identifies them as fugitive traitors. The problem is that poster cannot have been there. Varrick and Bolin escape in the previous episode (Battle of Zaofu) but are captured minutes afterwards. (So, no posters needed.) The next day, they escape again by blowing up their imprisoning train car. Their captor, Bataar, thinks they are dead. Indeed, Varrick intended to die. Later, Bataar is actually shown reporting them dead. One might argue that the poster wasn't a wanted poster, but one that warned people about the empire making an example of the traitors.This argument is too flawed: The empire had many examples already, some very high-profile. And a propaganda poster must be placed in plain sight, not in a security booth corner especially designated to let security guards compare the passing individuals. (00:14:00)

Plot hole: In each episode, Emmy, and Max travel to dragon land (often for a long time) without their parents ever knowing. This makes no sense. Their parents would notice sooner, or later that Max, and Emmy always go in, and out of the house, or that it's always quiet in Emmy, and Max's playroom. You'd think Emmy, and Max's parents would get suspicious, and would question their children accordingly.

Thank Heaven for Little Girls and Big Ones Too - S1-E4
Plot hole: "Three Tahitians", one of the masterpieces from one of the most famous post-impressionist painters in the world, is authenticated by an ordinary school teacher. Because that's the person for this multimillionaire job, obviously. (00:25:20)

What If... Ultron Won? - S1-E8
Plot hole: At the end of the previous episode, the Watcher gets surprised (literally saying "wait, what?") by the arrival of Infinity Ultron inside Party Thor's universe.In this episode we find out the story of Ultron.Ultron realises for the first time that there are other universes to conquer right then because he can'hear' the Watcher talk (to whom?) and goes after him.So the two episodes don't match;Ultron couldn't have reached the other universe "before" his realization, and Uatu is again surprised by it.

Plot hole: During the episode "Superstition", Onizuka thinks he has cancer because the magnetic pain-pads he was wearing created strange blobs in the X-Ray he has taken. However, given the fact that the X-Ray was so strange, doctors would have given him a complete physical, and noticed the pads much sooner. Here, they literally just assume he has tumors, and fail to ever take notice of the pads. Simply impossible, given the gravity of the situation. (Obviously, this is to pay off at the very end of the episode.)

Plot hole: The Skrull base is inside an abandoned nuclear power plant with enough radioactivity to force any human (like, say, Nick Fury) to constantly pop iodine pills to fight the symptoms of a poisoning that would kill them in less than half an hour. Despite that, Skrulls also detain prisoners, for years in some cases, in rudimentary shackles without any sort of shield or protection against the radiation.
Suggested correction: Iodine pills don't fight the symptoms of radiation poisoning; they prevent the body from absorbing radioactive iodine. It does not protect from exposure to radiation; it won't save you from it. Secondly, it's all an act by Gi'Ah posing as Fury anyway. Thirdly, they are in the reactor control room where Gravik says the radiation is higher. The prisoners are in a low radiation room, which could be extra shielded from radiation. It could also be that the prisoners are fed iodine to block radioactive iodine.
We can make up if we want that there's a special, super-secret anti-radiation serum and/or super-effective shielding, helping humans even during an exposure that lasts years (a decade in the case of Rhodey!), but there has to be something in the actual visuals that remotely hints at it. It's hard to headcanon that the dingy area of the plant where they are racked together, strapped to bed nets behind tarps, can be "low radiation", or that they are given anything to counter it. In particular, in the ending, the rescued people leisurely walk around the plant with zero radiation protection, even casually in the open yard where "Fury's" Geiger counter was going mad earlier. And the radiation was not something induced by the Skrulls that just ended when the baddie died. Not only is there no techno-babble justification (one could argue it's simply a pedantic detail not unlike the lack of hair growth or muscle atrophy), there's a direct flagrant contradiction in how the environment of the location - which is the only reason why they picked that site as a base - is deadly to humans only to a dramatic degree only when it's convenient.

Revenge of the Rogues - S1-E10
Plot hole: During the fight at sundown, Cold gets a hit on Flash and he goes down. Eddie takes a shield and goes to help. But Flash was in the middle of the street with no obstacles around, and it's implausible that Eddie could have gotten to him without Cold or Heat seeing him.

The Wedding of Iron Man - S1-E13
Plot hole: When Mandarin is concluding that Tony Stark and Iron Man are one and the same, he is watching video footage of when he had Tony Stark captive, and Tony first constructed the Iron Man armor and used a dummy that looked like himself in order to fool Mandarin into thinking that Iron Man was rescuing Tony Stark from captivity. If Mandarin had video footage of Tony Stark in that room where he organized his own rescue, then he also would have had footage of Tony Stark constructing the dummy of himself in the first place, and thus would have known Stark was Iron Man from the get go. (00:13:06)

Der Kampf gegen den Drachen - S1-E3
Plot hole: Shiryu states that the Dragon Cloth, which has been 'for eons' under the waterfall (let's just say it's an exaggeration) is harder than diamond and invulnerable to any attack. In the original manga and anime series, Pegasus uses a sudden dodge during a daring grapple to get Shiryu to strike his own shield with the glove of the armor, shattering both ("invincible sword meets invincible shield") and causing him to fight barechested. In this remake, this whole part does not happen, so when Seiya wins the fight with a heart punch like in the other versions, he does it when Shiryu has his heart still covered by the thick breastplate of the armor, making the whole "Shiryu's armor is impervious to any hit and much stronger than any other Cloth" plot point completely moot.
Suggested correction: It is only said that the "Dragon Shield" is unbreakable.
No, says much more than that. "That might be true for other armors, but the Dragon Armor is special. Nothing can get past my shield. It's unbeatable. The day my Cosmo forced the waters of the Lushan to flow upwards, it revealed the Dragon Armor. Battered for eons by the falling water, the Armor had grown harder and more radiant than a diamond. My Armor is the hardest substance known to man. No matter how fast or hard you strike, you've lost, Seiya." He parried the blow with the shield and so that deserves a special mention, but they keep mentioning the armor as having intrinsic properties, and he is wearing the armor when he is struck by Seiya, which guards his heart. In the original anime and the manga he was armorless after Seiya wrecked it, in here it's intact. It makes no sense, which is why I categorize it as a plot hole and not just as Character error: it's not that maybe he's wrong about the armor, it's the whole situation that now is flawed reprising the original with key differences.

Recognition - S1-E17
Plot hole: Bridge could have used his powers to figure out if Wootox and Sky's bodies were still switched.

Plot hole: Sydney is able to surmise from the artwork (we could also say from the writing, but her rival is one step ahead of her for 2/3 of the episode and it is established that he does not know the language) the precise location of the koi in Lumbini. The map is 150 years old, but there's no way even with a big stretch of imagination to buy that they both'd be able to pinpoint with such ease and certainty its location in the basement of a random building in the bustling market center of a town, that surely changed plenty during the past century and that does not bear any special landmark.

Plot hole: During Ryder's report, as Bruce and company watch it on TV, the camera suddenly zooms in on Joker standing on a catwalk above Ryder, and none of the crew, especially not the camera man who caught the villain, makes a comment about this. They may have thought the Joker (or rather an impersonator) was perhaps a surprise gag in the show, but since this is supposed to be a serious documentary report, it is still strange that they wouldn't point it out.

Invasion of the Punk Frogs - S2-E8
Plot hole: Shredder meets the frogs for the first time and gives them clothes using the holographic projector. The frogs continue to wear the same clothes for the rest of the episode, even without Shredder being around.