In the final battle, Darkseid Omega-Beams Kara into unconsciousness. As he leaves her, she's lying face-up. But when Superman sees her, she's lying face-down.
How does Darkseid know Superman's real identity? This is never explained and Superman is well known for hiding his identity from public knowledge. It's never explained how Darkseid knows where the Kents' farm is and how he follows Supergirl and Superman to it. It's just left unanswered.
Why isn't Darkseid sent into empty space in other films like in this film? Supergirl has a brilliant idea to rewire the Mother Box and send Darkseid into empty space. This doesn't seem to happen in other movies that feature Darkseid. A good plot point but if it worked in one universe, it should work in all of them. It makes no sense that this isn't used more.