It could be hacked but I can't really be certain unless you give me more information such as it's IV's, Shininess, Moves, OT, Original Trainer Name, Where is was Obtained, The Date, Location and Origin Game.
It could be just a glitch but if it is hacked don't get rid of it because if it was that much of a problem then it wouldn't of made it through Pokémon Bank.
You could try changing Shaymin's Forme from Land Forme to Sky Forme as that should hopefully change it's Ability as well. You can change Shaymin's Forme with the Gracidea Flower.
>In Pokémon X and Y, Gracideas are featured in one of the paintings on display at the Lumiose Museum. A female NPC located at the Snowbelle City Pokémon Center will share one of her Gracideas with the player if she is shown a Shaymin.