Another thing Is that Green lantern Is brainwashed by Brainiac, While Flash not.
We could Say that at that Moment only Green lantern Is "evil", but Amanda Waller still gives the order to kill the League. So my theory, the people Who were taken by Brainiac by the time that the Squad shows up are Superman and Green Lantern. Then Flash Will be taken, followed by Batman, and Wonder Woman Will be a recruit, Like penguin. Also the Speed force guntlet comes from dr. Sivana.
In one trailer, Batman visibly hesitates a punch, like he's resisting the mind control. I mean, it makes sense since he's fought Scarecrow, Mad Hatter and Joker in his mind multiple times now.
Anyway, with continuity regarding the movie and comics, my personal views is to not worry about it. This is comics, we can literally create an explanation for anything. Regeneration, alternate timelines, alternate universes, clones, identical twins, it doesn't really matter. I mean, Joker could literally come back to life and it wouldn't surprise me (don't do that though, lol).
Captain Boomerang was dead, now he's alive again. Enjoy your game.