User blog comment:Thailog/Ep. 206 "Bloodlines" discussion/@comment-174.228.134.151-20120603072051/@comment-432124-20120603193549

It wouldn't be illogical for them to exist in the future if the future they exist is an alternate future. From their slang, the aliens that were controlling Neutron seemed to be from the future, so they could have been from the Legion's future and they could have messed things up while the Legion was away. And since the Legionnaires and the aliens would have been in the past, they wouldn't have been affected by all the changes in the future. If it had been otherwise, then Bart would have somehow been affected by the changes that he made to the future while he was in the present, but he wasn't.

And as for changing the events of certain past episodes, that could possibly be the whole point. They wouldn't have to change the events of Season 1, but if some of the events of Season 2 were the results of the aliens' tampering with time, then those events weren't supposed to happen. I know that it may be out of place for some people, but some shows, like Wolverine and the X-Men have done it well.