It is said that the Swords of Justice fought a battle against people. Seeing as they spent a lot of time fighting with the people, they may have probably learnt their language, as they are legendary and highly intelligent creatures.
However, this could also be telepathy. Many legendary Pokemon speak via telepathy, such as Jirachi from "Jirachi the Wish Maker" and Shaymin from "Giratina and the Sky Warrior".
Another possibilty could be that the Swords of Justice speak to each other in the Pokemon language, and that the film is translating what it means. Because, to be honest, it would be quite boring if all you could hear was "Vi-vi-Virizion!"
These are just theories, however.
Hope I helped :D