How can Tobias in Sinnoh League Champions ep.658 own Latios? Latios, as a legendary Pokemon, appears only once in the whole Pokémon world and, for we all know, he is dead since the Pokemon Heroes movie?
Although they are called "legendary", these Pokémon are not necessarily unique in the anime (or in the games). A good example is Silver, which is a younger Lugia. Tobias most likely has a second Latios.