Game-Breaker: the Zhon faction has the best defense turrets in the game - powerful, long-range, quick to build and relatively cheap. It's entirely possible to advance by building just those and a few "artillery" units, and they're a huge pain to deal with even when used just in their intended role.
Veruna is rather overpowered in the vanilla version of the game, presumably because their hat is the sea, the creators didn't want them to be disadvantaged on all-land maps, and overcompensated.
Good Bad Bugs: Unlike the metal wrecks from Total Annihilation, corpses in Kingdoms fade away over time...unless the unit died on the coastline. A glitch means that any corpse touching water never fades, giving you more time to get a resurrection unit there.