biters suddenly start spawning inside factories (even on belts and train tracks).

Same here, spawners just appeared inside my base between assemblers even, I also found one spawner in the middle of ocean (it wasnt there before).
Got really surprised when I got to gleba and my base started blowing up :p
Only other mod doing anything with enemies in my game should be Entrenched Enemies.

Were there any improvements?

Sorry for the late response, but were you running Space Age?

Hey, getting same problem. when i travelled to another planet there nest spawning just inside my base like worms or titanic biter nest just inside belts

Next version should fix that, and it will be releasing soon. Alternatively, you can go here: https://github.com/modded-factorio/bobsmods/tree/dev

Click on the green "Code" button and select Download Zip. Then find the bobenemies folder inside the zip file and replace bobenemies in your mods folder with that.