PokéBase - Pokémon Q&A
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Mega Mewtwo Y was probably a different forme to Ash and everyone, and they didn't know what Mega Evolution was at that point
It was eclair forme at that point. Besides, that Mega evolution created a huge platform for XY.

This isn't the first time they have done something like this though. Zoroark appeared in a Gen 4 movie and Ho-Oh appeared in the last episodes of Gen 1 anime, despite neither belonging to that generation.
Zoroark is Gen v.....
A similar question to this was already asked by me

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Well, this is because each and every last movie of that particular generation creates a spoiler for the next generation. Below are the spoilers for the next generations each:-
Original Series -- Latias and Latios
Advance Generation Series-- Lucario (movie 8), Manaphy and Phione (movie 9)
Diamond and Pearl Series-- Zoroark
Best Wishes series (Black and White series)-- Mega Mewtwo Y (some thought the boost form or just me.)
Thank you

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It's just for the sake of publicity.

They have actually done it before with Zoroark.
As for the Mega evolution. They have now explained that Mega evolutions existed before 6th gen. It's just that nobody knew what they were at that time. That is shown in Pokemon Origins (1st gen), where Red evolves his Charizard into Mega Charizard. Crazy right? Only if we had a Mega Charizard when we played Pokemon Red Version.