Many people are reporting the same problems on the Steam forums. Hopefully once the developers have had some rest they can start looking at tracking and applying some bug fixes.
Some of the faction increases and decreases seem wonky. When meeting the 'mistaken identity Marcus' (The Marcus with a 'C') in Saturnalia, as an Iscari, all combination of dialogue responses lead to a significant Golgotha faction decrease. The only way to avoid the large faction decrease is to choose the initial option, "I'd rather not, actually." and avoid the encounter entirely. *shrugs* Maybe that's not a bug but just Golgotha weirdness working as intended!