More often than not, the anime/movies are inconsistent with the games. For example, in the movies, there are multiple Lugia and multiple Mewtwo. My theory is that some of the lesser legends, like the Regis and Azelf, Uxie, and Mesprit have multiples. My reasoning behind this is that they require less energy for Arceus to create them, and they represent integral parts of human culture. So wherever they are needed, wherever human civilization pops up, Arceus creates them. But there only needs to be one master of time, space, sun, rain, etc. so Arceus doesn't create multiple of the cover legendaries.