Would it even be feasible to beam up a swarm of bees? I mean, while they are physically small, each bee is a individual, complex, living creature. Every single one would have to be individually scanned, broken down, and its pattern stored (albeit briefly). Does the transporter have anywhere close to enough memory to beam dozens--maybe hundreds--of individual creatures up at the same time?
Just because the creature is physically much tinier than a humanoid doesn't mean that the computer file that descibes it is proportionally smaller.
(I may be overthinking this.)