If you look close enough, every movie will have some plot holes sprinkled throughout the narrative. The MCU has had mix-ups with their stories and so does DC. As soon as fans look too much into the small details, it can ruin the experience.
While some of the plot holes in the DCEU have had the directors come to their rescue to set the fans straight, others require fans to have an open mind and not be too critical. There have also been times when there have been perfect, logical explanations for on-screen miss-haps.
Batman V Superman
One of the plotholes mentioned by fans watching Batman V Superman, and the only difference that the audience was made aware of was the two learning that Lex was manipulating them.
In fact, the entirety of the "Martha" scene was pivotal in Batman recognizing the humanity within Superman. Also in Justice League, even if Bruce still hated Superman, he's intelligent enough to know that the good that Superman could do for the world now outweighs the personal grudge that he had in the previous movie.
Superman's Amnesia
One of the main elements of Justice League was Superman's revival, which involved showing fans Superman taking on the rest of the Justice League. It could be questioned how Superman ed Batman when he appeared after Superman's resurrection but had no recollection of Wonder Woman.
The answer seems to be twofold: One, because perhaps Superman's amnesia is not a simple as not ing anything. But also, the events of Batman V Superman, specifically Batman's rivalry and battle against Superman, make him a key part of Superman's memory.
Aquaman's Air Bubbles
The plothole surrounding the Atlanteans comes in the form of the following question: why do the Atlanteans need air bubbles to speak if they can breathe underwater?
The simple explanation is that it has nothing to do with the Atlanteans breathing, but potentially more with the physics of sound and its lack of ability to travel the same in water versus air. Yes comic book movies have not been too concerned with the accuracy of Physics generally but it's always nice to make some effort. Not to mention that it makes for great VFX.
Whales Near Explosions
In Man of Steel, some fans were confused as to how the whales were coincidentally in the same place as Superman when he fell from the oil barge in the middle of the ocean after saving the workers. Usually, if there was a giant explosion, whales would likely swim away.
Jason Momoa has answered this question himself explaining that it was in fact Arthur Curry who saved Clark Kent by communicating with the whales.
How Darkseid Forgot Earth
Most recently in Zack Snyder's Justice League it was shown that the Anti-Life Equation was on earth. It also showed that Darkseid tried to conquer earth in the past by battling against the Gods, Amazons, Atlanteans, as well as the Green Lantern Corps.
Many fans were left wondering how Darkseid had forgotten the Anti-Life equation was on earth. This has also been addressed by Zack Snyder, who explained that the original battle was an incredibly long time ago, and also that the army he fought with at that time had been killed.
Where Are The Suicide Squad?
One of the age-old questions in comic book movies is "Well if the world was in danger why not call X other superhero?" or "Why did X not phone Y when this was happening." The answer is simply because it is not their movie. Even if the Suicide Squad was set in the Snyder-verse, that doesn't mean that they absolutely need to show up to exist together.
Some fans question why other superheroes (or in this case, villains) are the ones who would have an issue if the movie didn't focus enough on a certain character. Adding another 5 or 6 characters to the mix of the movie would cause writing mayhem.
Why Batman Kills
One thing that Ben Affleck's Batman does that strays away from the Dark Knight from the comics is his capacity to kill. Fans saw Batman kill many people in Batman V Superman: Dawn of Justice, which has caused some fans to be uncomfortable, especially as Bale's version emulated this aspect of the character.
As well as Zack Snyder's explanation of why Batman kills, keep in mind that Ben Affleck's Batman is a much darker Batman than what has been on screen before. Also, it is not the studio's job to make a Batman that is "as close to the comics as possible". It is their job to make the best movie, and if Batman killing makes his character more interesting, darker or serves the story then that's what should happen.
Clark Posing With The Red Cape
Way back in Man of Steel, fans saw a young Clark Kent posing with a red cape, seemingly mimicking Superman. Of course, it didn't take long for some fans to ask why Clark was wearing a red cape if Superman didn't exist in this world.
In the world of 'keeping an open mind', Clark could have been emulating a Roman soldier who also wore red capes, or potentially even Thor as Marvel does exist as a comic company in the eyes of DC. Or maybe he thought wearing a cape would make him feel more like a superhero. These are just a few logical explanations for the red cape.
"Martha"
The infamous "Martha" scene that some fans loved and some hated. For those who were not a fan of the scene, Clark saying "Save Martha" showed Bruce that Superman did have a human side with a mother who he loves, as all other humans do.
Some fans have questioned why Clark didn't say "Save my mother." Perhaps because if he simply said "my mother" Batman could have thought he was talking about his Kryptonian mother, and Bruce was certainly in no mood to save other Kryptonians.
Why Did The Kryptonians Take Lois?
In Man of Steel, some fans pointed out that the Kryptonians had no reason to take Lois Lane onboard their ship in the third act if all they wanted was Kal-El.
However, the Kryptonians have likely monitored the planet they are about to invade and could easily have ascertained that Lois is the one who wrote about Superman and is one of the humans that knows him the best. If they needed to extract information about him or use someone as a bargaining chip, Lois is the one to go for.
