In the confrontation scene in the major's office with McDonough during "In Sheep's Clothing" (FFDiamondCity10), Geneva will turn hostile to the player after saving her if certain dialogue options are chosen by the player.
Choosing the following options seems to reproduce this properly for me every time:
(1) Enter Diamond City through the main entrance (not the city's exterior elevator), and then save Danny Sullivan by giving him a stimpack (not sure if this matters for sure).
(2) Enter the mayor's office using the elevator
inside Diamond City. Piper will be trying to break down the door. Unlock the door by picking it or using the hidden button under the desk.
(3) Choose the following dialogue options when McDonough is holding Geneva hostage: [a.]
Discarded? (don't use the persuasion option to convince him to let her go), [b.]
You'll stand trial (the mayor will go on about how he won't be held in prison and so forth), [c.] McDonough goes hostile. Shoot him and Geneva will then turn hostile towards you.
Note: If the player (or a companion) then goes on to kill Geneva, Piper (as well as everyone else in the town) will go hostile. This doesn't seem to happen if you allow Piper to kill her instead.
See
Issue #26287 for a game save to reproduce this issue. It's right outside of the main entrance to Diamond City.
Issue Data
Issue #26288: FFDiamondCity10: Geneva can turn hostile if certain dialogue options are chosen