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.
It's my understanding that Pokemon Heroes mentions that they come with their father and HE became the first soul dew. Not only that, but at the end, a Latias can be seen flying with two Latios, one her size and one larger. They could be another family, or perhaps the entire family reunited.