Other mistake: After realising they can track the mother box, Batman says they have to go back to his base to use one of his satellites to track it, and they all do so. Which completely ignores the fact that Cyborg could easily access the satellite feed directly using his abilities and display it to the others on any nearby screen in Star Labs.
Other mistake: Barry comes back to his home, replaces the fuse in the fuse box, flips the handle (begs the question of why remove the fuse AND turn off the switch, but whatever), and within 2 seconds every screen in the place is lit up. Sure, a TV might come on that fast, but plenty of those screens are showing data, analysis, etc, running off computers, which would take longer than that to boot up and get everything running.
Other mistake: Apparently, one of Aquaman's superpowers must be to be super-heavy, since surfing on the body of a parademon he lands on a five story building and that somehow slices the whole building in half, complete with explosions that leave him unscathed and don't turn the parademon's carcass into a pulp. (03:15:15)
Other mistake: Before Wonder Woman bursts into the room with the terrorists there's a cut to the schoolgirls watching the bomb about to blow. The girl to the far left is actually cracking a laugh. You may justify it as a hysterical reaction (she does the same in the foreground when the baddie turns the key), but appearing just in brief moments and with her looking properly afraid in other shots, it just looks wrong. Whedon's version didn't feature the corpsing. (00:20:40 - 00:21:35)
Other mistake: In this version, Queen Hippolyta whispers "Return to me, Diana" as she shoots the arrow, as opposed to "Listen to me, Diana" in Whedon's version. Whedon's line made sense, since it was a warning, this does not, since Diana never comes back to Themyscira nor she is supposed to, being busy thwarting the invasion in the Land of Men. There's no reason why the Queen would say that line. (00:43:10)