Plot hole: The heroes find Steppenwolf's base thanks to Cyborg's dad, who superheated the core of a Mother Box so it shows up on a thermal scanner. But the box itself wasn't emitting any heat on the outside, and a satellite can't magically infer the internal heat of an object if it's not conveyed to the surface. If Wayne has such precise satellite sensors, it would also spot a nuclear plant suddenly drained from radiation, and the intense energy (and heat) caused by Steppenwolf's activities.
Revealing mistake: When the military security checks Flash's phony badge, the name on the personnel list to the right does not match the fake identity; Barry's false identity is "Rowe, Wesley", but in the list the name "Band, Ryan" is highlighted. This mistake was not present in the theatrical 'Whedon' cut where the name was altered to match. (02:27:05)
Continuity mistake: After the underground battle with Steppenwolf when they are finally joined by Aquaman, Wonder Woman sums up the situation with "All he needs now is the Lost Box of Men." Batman replies "If he doesn't already have it" in another shot, where Diana's hair is missing in front of her shoulder. (02:08:25)
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)