There is only one of each legendary that the player can catch in each game to avoid a player having too many legendarys and making legendary Pokemon somewhat rare.
However, in the anime it has been shown that multiple legendarys exist such as the episode where there is a whole field of Shaymin. Also, characters in the anime often say things such as:
"Hey, it's a Manaphy!"
instead of :
"Hey, it's Manaphy!"
This implies that there is more than one Manaphy.
(not real quotes)
The reason that they make a big deal of legendarys in the movies because if they were weak the movies would be boring and no one would watch them = no money made.
