So in All-New X-Men they kept on talking like the original X-Men being in the present would change the timeline, but it's always been a very well established rule in the Marvel Universe that any changes to the past only create alternate timelines and don't retroactively alter the present.
*Age of Ultron Spoilers*
Now in Age of Ultron Wolverine was able to go back in time and kill Hank Pym to prevent the creation of Ultron in the present.
So I was wondering why they would change such a fundamental rule in their universe, and then I thought about if there could be any recent events in comics that would have caused it. Eventually I remembered something that happened in New Avengers.
While trying to stop the universes from clasping in on each other this happened.
Now all the Infinity Gems were shattered but the time one just vanished. Now According to Reed Richards the Infinity Gems are a constant tied to the existing to the universe and trying to destroy them would cause the universe to react. I believe that this even is what has changed the flow of time to allow the past to change the present like in AoU.