Mild spoilers ahead, obviously.
1) When you first go meet Takemura at a Diner, Johnny appears and tells you that he will no longer try to kill you. The problem is, if you go around the city before that, Johnny will interact may already interact with you as if you are best buds. This happens if you go pick up your car from the garage or if you meet a guitar player on the street and get a quest to find Samurai vinyls.
2) In the Cyberpsycho Sighting: The Wasteland in your debrief with Regina both of you refer to Saul being taken prisoner by the Raffen. This happens even if the player has not started that quest yet.
I am sure there are more issues like that.
1) When you first go meet Takemura at a Diner, Johnny appears and tells you that he will no longer try to kill you. The problem is, if you go around the city before that, Johnny will interact may already interact with you as if you are best buds. This happens if you go pick up your car from the garage or if you meet a guitar player on the street and get a quest to find Samurai vinyls.
2) In the Cyberpsycho Sighting: The Wasteland in your debrief with Regina both of you refer to Saul being taken prisoner by the Raffen. This happens even if the player has not started that quest yet.
I am sure there are more issues like that.