>>12846731I think there are multiple of the Legendary Birds and Beasts, unless you believe Ho-oh raised the only three, but that would contradict the Dex entry for Entei. There are multiple Deoxys, possibly multiple Mew as it's believed it was once part of an entire specie. There's only one Mewtwo unless some stole the cloning information from the Cinnabar Island lab or Giovanni decided to try and clone another one, which is doubtful given the catastrophic failure of the first. Only one of each of the Weather trio ad Ho-oh, I once heard there was a baby Lugia in the anime but I didn't watch it so that could be horseshit. Don't know about Jirachi or Latios or Latias.
There are probably multiple Manaphies and Phiones due to breeding, but beyond that I'm not sure. Not big on Gen IV or V lore.