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 Clark's real identity??? This is never explained and Superman is well known for hiding his identity from any public knowledge. It never explains how he know were the Kent's farm is and how he follows Supergirl and Superman to it. It's just left unanswered.
Why isn't Darkseid sent to empty space like in this film in other films? Supergirl has a brilliant idea and rewires the mother box, and sends Darkseid to empty space. This doesn't seem to happen in other movies that feature Darkside. 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.