*Spoiler warning*
In the first mission, you sneak into a whale oil processing plant where the workers are on strike for better pay and the greedy capitalist who runs the plant is trying to crush the resistance by torturing the workers with shock treatment. You encounter the leader of the striking workers being intimidated and coerced by the factory owner. I sleep darted the factory owner and spoke to the strike leader, who stated that if I help her blow up the factory, she would give me valuable information you need for the real plot of the game. A message also appeared stating I could put the capitalist pig in his own torture chair as an optional side mission. Naturally I decided to do just that. However, after making the 1%-er "ride the lightning" until he talked, and receiving the information, the waypoints for the bombing disappeared and the waypoint for exiting the factory to end the mission appeared. There was no reason I shouldn't have been able to also bomb the factory and hear additional dialogue from the strike leader. Furthermore, the torture objective was listed as "optional" thereby implying it was an extra objective, not a replacement for the main objective. I was also not about to replay the section to see what would happen if I bombed the factory instead, because then there'd be no electric torture chair for the "optional" objective.
TL;DR - I wanted to kill a robber baron and destroy his factory, the game wouldn't let me do both for any explicable reason, and I'm not completing this DLC