Answer 1

There have been many instances of this occuring. Such as Lance's Dragonite at LV 50 when it evolves at LV 55 in the Elite Four in Hg/Ss. GameFreak did this for one main reason.
They wanted to make the game more challenging.

Answer 2

GameFreak does this with every game, they just do it to make the game more difficult.

Answer 3

That's how Gamefreak desighned the game to fight Ghetsis.There's no explination to say that the game is glitched. (HOPE THIS HELPS!) :)