In the mutant questline:
The small sentry bots in Kirril's lab use stingball grenades instead of flashbangs. This is not a bug, however they do not drop stingball grenades and instead they drop flashbangs on death if they havent used their stingball grenades yet.
Killing Kharon on the docks after he takes you to the black sea mutant island, softlocks the game. Wesley and Doctor M repeat their dialogue and the game never ends requiring a reload
BONUS:
If you play as Aegis throughout the entire black sea questline, and have no casualties at all throughout the DLC (achieved by being a very high level character (basically killing all the natives efficiently) AND pickpocketing the technicians walkie-talkie to prevent the death of the arch island keep aegis guards) causes aegis to leave but leave behind the 3 jet skiers that orbit the island. They keep their consistent patrol route even though aegis has left the expedition already.
