All bees have specific requirements to work in. Two of these are temperature and humidity. Biomes have different values for these. The Plains biome you start out in is a comfortable temperate climate with Normal temperature and Normal humidity, perfect for bees that don't have any specific requirement, like the Rarest Bee or the Meadows Bee.
However, if you try to put a Marshy Bee to work in this biome, they will refuse to work because they require Damp humidity and Normal temperature, found around rainforests, marshes and swamps. Similarly, certain bees require Hellish temperature and Arid humidity, which can only be found in the Nether.
Until you can mutate your bees to be more tolerant of the Plains biome, extend your base out until you find a biome that can support the bees you want to work with. You can see exactly what temperature and humidity the biome supports by placing down a Bee House or Apiary, and then clicking on the climate button on the top right of the GUI.