Which was Luthor's plan, exactly? He manipulates Batman to fight Superman, and creates Doomsday in the meantime. If he expected Batman to kill Superman, why does he create Doomsday? And if he expected Superman to survive his fight with Batman, why bother with it at all? And let's say that Doomsday does kill Superman. Then what? Is Doomsday supposed to be less of a threat than Superman?
Batman has studied Superman for YEARS. Right or wrong, his notion that he's a grave threat is solid and well fundamented. So why does he change his mind when he simply mentions his mother? He is still a nigh-omnipotent alien, capable of mass destruction.
What would Superman have said to the comitee? Does he submit to the government control? Does he do what he thinks is right? Team Iron Man or Team Captain America? The explosion leaves us without answer.
I can understand Raven or Zatanna having prophetic dreams, but Batman? He's just a common man! He can't have those dreams. Also, Team "protect the future", or Team "change the future"?
So, Batman is now a psycho killer. I can understand that, even if it isn't the Batman I have usually seen. But then, if Batman does not have a problem with killing, why is the Joker still alive?
Why does Luthor need to set up a trap to frame Superman for being destructive? The guy obliterated a whole city, for God's sake! Does he need to do that all weeks so people remember that?
Why is Wonder Woman so interested in that photo? WWI was a century ago. If nobody noticed in a whole century that there was an Amazon warrior out there, nobody ever will. And she should have done this some decades ago, when photos were a physical thing. Now that they are digital, her quest is pointless. A computer file in a place like that surly has lots of backup copies, and even a deleted file may be retrieved from a device if really needed. But the photo is not a good proof of anything, anyway. It's just a woman with a spear and a weird clothing.
Why Perry isn't interested in a story about a violent vigilante costumed like a bat, and wants to talk about sports instead? Isn't his newspaper supposed to sell newspapers? Perhaps the Daily Planet should fire him and hire J. Jonah Jameson instead.
Flash comes from the future and says "You're right about him. You've always been right. She's the key, Lois." That doesn't make sense with the events of the film. Lois convinced Batman that he was wrong, not that he was right. So what the hell was Flash talking about?
In all the time that Batman has been preparing for the big fight, why didn't he discover his secret identity, or his relation with the Kents, that such reveal came as a big surprise? So much for the "world's greatest detective". And now that we are at it, how is it that he did not notice the activities of Lexcorp, and he's easily manipulated by Luthor? Let's say that clear: LUTHOR MANIPULATES BATMAN. I have a bad feeling about this...
Things that don't make sense in Batman v Superman (spoilers!) (duh)