Basically the entire movie takes place after the events of Justice League Unlimited the same universe as JLU, but neglects the fact that the League is aware of the Legion of Super Heroes. In the JLU episode “Far From Home,” Supergirl, Green Arrow, and GL John Stewart were sent into the future and assisted the Legion in defeating the Fatal Five. After their adventure, Supergirl stayed in the future. Not once in the movie do they mention knowledge of the Fatal Five, the Legion, or Supergirl and her whereabouts. That’s a pretty big suspension of belief Eric Carrasco is asking of viewers and just goes to show how lazy his writing was for this movie.
Also they just kinda shoehorned Miss Martian in and she just feels super out of place.