Believe it or not, those are an actual, literal species of bee (as in, the animal) called the grub bee—so named because it was often misidentified as grubs thanks to how pale they are and how they tend to wriggle about within the vespiquen hive. Yes, these are actually perfectly ordinary animals. Why they react to poké balls as if they’re a part of their host vespiquen is actually a mystery that scientists are eager to solve, if only because that would mean fascinating things for Kingdom Animalia as a whole. (Can other animals enter poké balls if they form symbiotic relationships with pokémon? Can humans? I, for one, would love to know the answer to the latter especially. After all, who wouldn’t want to know what it’s like inside a poké ball?)
To put it in short, vespiquen forms a symbiotic relationship with grub bees. In exchange for serving as a living hive (and also protection from birds of both the pokémon and animal variety, as well as a food source to ensure that the grub bee never leaves), the grub bees defend vespiquen on command or use their royal jelly to heal her. Usually, this relationship will begin shortly after evolution, so if you’ve noticed your vespiquen flying low to the ground, you now likely know why: because she was attempting to attract a grub bee queen. Once she finds one, this relationship lasts essentially for life, with new queens replacing the old every year. So in a sense, if you train a vespiquen, you’re not simply training one pokémon but a whole hive, which is really quite remarkable.
The Pokédex According to Bill 