I know that in the world of comic book things don't always stay the same and things fluctuate. But these are some things that, to me don't make sense even in their own world.
Batman: I know Batman is at peak physical form. He's is as powerful as a human can be without being super powerful. But it still doesn't make sense when Batman punches or kicks someone MUCH stronger or durable then he is and it actually affects them. Being that take blows from people much stronger then Batman and not fall, yet and still they take a punch or kick from Batman and it actually staggers them. Batman uses alot of explosive batarangs. I can understand these working on a normal person or someone enhanced like Bane. But why don't these work or creatures like Parademons? I have to imagine that they are pretty durable and that regular sharp object aren't going to stick in their skin, but batarangs do. I also have to imagine that a few explosives aren't going to bring them down.
Another is if Batman has to come up against and magic creature or demon. He'll use exo-armor to fight said creature. Exo-armor will use explosive rounds and electricity as weapons and Batman'll win. But...why? Why would a demon be affected by electricity or explosives?
Wonder Woman: We see Wonder Woman slapping around gods in her book but how? Wonder Woman was basically granted her powers by the gods (when shes not a half god or New52/DCYou God of War) Couldn't they just take her powers from her? Even as a half god she still shouldn't be able to slap around full gods like Ares. I can't imagine the gods granting her powers equal to theirs. And if Diana and the other amazons worship these gods as their supreme being then why doesn't she try to stop what they are doing? Even if they killed half a country, wouldn't that be considered divine punishment because of her beliefs?
Green Lantern: It is said that the ring can do anything. But all we ever see it do is make hard light constructs. The ring is pretty much and device that can alter reality. Really, it should be able to solve pretty much any problem. Maybe the users just can't come up with anything really clever to do with them, I don't know but it sure seems like all its shown doing to making constructs.
Cyborg: If Cyborg is always "plugged in" shouldn't he have just about ALL knowledge on Earth? Shouldn't he be the smartest, and if not the smartest, the most knowledgeable being on the planet?
I'll come back and add more at a later time. Please feel free to add something that don't make sense to you.