For several versions now, the default flier count has been very high. Most servers have an issue with the amount that accumulates over a period of time. The issue causes FPS issues even for those with the most intense of computers.
Perhaps adding an option to limit the amount of fliers around each player to the BetterSpawner config could remedy this situation.

This is more of a suggestion than a bug so if you'd like an option that limit fliers spawning to be added then you can suggest it on our suggestion forums (https://pixelmonmod.com/viewforum.php?f=146). Note that the config settings "maximumSpawnedPokemon" and "entitiesPerPlayer" both provide a type of solution, though not what you were specifically looking for.