Most likely it is just that specific dual dialogue that was affected.
There are a couple dual dialogues on the starting beach (once after reading a diary and then another after the first fight), and possibly another depending on how you handle the drunk guards at the bridge.
If you reload the autosave made at the start of the game, if it hasn't been overwritten, does saving after triggering the dual dialogues eliminate the marks again?
There are people who save before every dual dialogue so they have the option to reload until both characters get the traits that they want them to have, while also getting the results that they want, where applicable.
