No, Manaphy is a Sinnoh Pokemon. It is #490 on the, the National Pokedex, and is only obtainable on Gen. IV and Gen. V games.
As for the Movie, I've never seen it, but I know that Pokemon Movies and the TV series are not in order. They may have seen Manaphy before they even reached the Sinnoh region, or while traveling to it. Here is a link on Manaphy if you want to know more.