Well then, there you have it, that proves it even more correct that Pokemon can do what they like and they have a will of their own.
Although, considering the anime/movies I agree, but I think those legendaries like articuno,raikou ect only acted malevolent because they were wild beasts after all and they were just trying to protect their own territory.
While the others such as Darkrai,Mewtwo, Rayquaza ect. I guess they had their reasons for being the way they were.