When Green Lantern is outside anchoring the Legion's base to the ground, Superman is breaking into that same base to free fellow league members, and among those trapped inside we see Green Lantern.
Rapid aging would not cause Superman's hair to suddenly go gray as shown.
The origins of Cheetah, Giganta, Lex Luthor, and most especially Bizarro are tied into the origins of Wonder Woman and Superman. Without a Wonder Woman and a Superman, there shouldn't be a Cheetah, Giganta, an evil Lex Luthor, or a Bizarro, but the villains are unaffected by the changes in history.
Superman flies to Krypton's former location in the Supermobile to obtain blue kryptonite in order to reverse the effects of the red. During this time, he gets weak from the surrounding green kryptonite and manages to successfully reverse the aging process. Later, the three villains look for Superman at the same spot, staying away for fear of what the kryptonite could do to them. Miraculously, all four of these people have their super powers at Krypton's former spot, yet no Kryptonians had any powers before Krypton was destroyed.
If Hal Jordan didn't become the Green Lantern of Earth Sinestro wouldn't have become his Arch Enemy or be a member of The Legion of Doom.
When Cheetah becomes Wonder Woman there's no Invisible Jet for her to fly to America.
When Superman appears near the end, Scarecrow is surprised and comments that he shouldn't exist. With Batman stopping the Legion Of Doom's attempt to alter the trajectory of Superman's rocket, Superman should indeed exist, and Scarecrow should still have memories of him existing as well, right up to this point.
When the Legion of Doom is watching Batman and Robin on their viewscreen (just after Wonder Woman disappears), Robin's chest insignia is missing.