Plot hole: When Cyborg tells his origin story, he says that the Mother Box in possession of the government was shelved till after the night when Superman died, when it came to life leading it to be studied by Cyborg's father, Silas. However, that contradicts the previous movie, Batman v Superman [both 1 h 39' and 2 h mark], where Batman came upon Luther's metahuman evidence file, including Silas Stone's vlog with the creation of Cyborg that Diana watches. (01:02:35)
Continuity mistake: When Wonder Woman says "He's back" looking at the freshly resurrected shirtless Superman, the policeman by the patrol car is leaning against it differently compared to the previous line-up shot; he was lowering the hand with the radio, and he's on the contrary talking on it now. (01:13:35)
Continuity mistake: Aquaman puts Clark's body in the amniotic pool. The photo of his father falls in the water-like liquid and begins to sink, and quickly. Minutes pass with the hacking and all the discussion in between on how to power the process, but when Flash finally 'jumpstarts' the machine, a shot is dedicated to the photo that is still there in the pool, yet to be submerged. (01:10:35)
Continuity mistake: Steppenwolf sends away the parademons saying "This one is mine" to confront Wonder Woman one-on-one. She says in close-up "You overestimate yourself" and her right shoulder is clear of hair, but in the previous shot she had hair right in front of that shoulder. (00:54:55)
Continuity mistake: When Flash calls himself "a snackhole", he holds the pizza carton with the hand at its corner, then more towards the middle. (00:38:45)
Continuity mistake: When Aquaman dumps the sailor that was attacked by parademons, the man has no green stains on himself, but he exhibits large ones in a close-up, not to mention that Aquaman's hand is clean in the rest of the scene other than the glass close-up (as we can see from the Snyder cut, the encounter had nothing to do with parademons in the original concept). (00:42:40)
Continuity mistake: When Wonder Woman breaks through the door, the left side flies off, sliding on the floor almost all the way to the couch in the reverse shot, and is closer to WW in the next. (00:09:45)
Continuity mistake: When Momoa says "He's not all right" commenting on Superman's shifty eyes when he's scanning them post-resurrection, his hair sits differently on his shoulder compared to the wider shots. (01:14:10)
Answer: "Surely they'd figure it out" is hardly a suitable solution. If they knew how to destroy them, they would have. They did the next best thing by hiding them in different places.