Three related ideas here.
1. Savage biomes could see seasonal
invasions by huge swarms of biome-appropriate vermin. These try to path to your food stocks, farms, daycare facilities, or other appropriate targets (or alternatively, spawn right on them if vermin pathing is an issue). Doors and traps are no obstacle to vermin, so alternative measures (small animal traps, trappers, cats) must be employed. Real-world examples include army ants, lemmings, locusts, and starlings. Particularly evil swarming vermin could inflict syndromes, too. I know that there are periodic explosions of some vermin, especially fish, but they generally pose no threat to a fortress.
2.
Invaders who bring nasty vermin with them. These could be snuck in (seems like a kobold sort of thing to do), smuggled in by vampires (the arrival of vampires in fiction is often associated with plagues of rats and other vermin -
example), or thrown in by besieging enemies. Vermin used offensively would obviously by of the vilest sort. I would love to see kobolds distracting pursuers by throwing scorpions and whatnot at them, just like in Kobold Quest. Goblins could replace stolen infants with writhing maggots or sneak deadly spiders into your mayor's bedroom, just like in
Dr. No.
3.
Invaders who are made of or
can turn into vermin. Forgotten beasts that trail vermin instead of causing syndromes directly or that collapse into hundreds of vermin when they're killed; vampires who turn into a swarm of bats and fly through gratings and bars to reach their victims and evade pursuit; etc.