The Rage Essence vial specifies two consequences, which as you noted may be resisted.
"Can’t tell friend from foe" and "Can’t stop until they’re all broken"
I think the first thing to remember is that these consequences are taken right away, so we can’t use them as the basis for new consequences - in other words, it wouldn’t be right to have their Skirmish roles have additional consequences for 4/5 rolls that they also hurt their friends. That might also happen, but I think we have to go back further. The fiction states that they can’t tell friend from foe, so when your Cutter says “I attack the thug that’s threatening us” you have to stop right there. This consequence is like a lack of information, so you can think of it like they’re fighting in pitch darkness and the Cutter can’t see who is who. If they take an Action Roll to hurt someone, it’s anyone’s guess who they’ll hurt. That sounds like a Fortune Roll to me, like you suggested. On a 1/3 it’s someone they wouldn’t want to hurt (and then they hurt them), on a 4/5 I’d say they might hurt a friend and a foe, or a less desirable foe (like maybe a piece of equipment, a civilian, or a weak support member like a clerk instead of the the mercenaries or guards that protect the area) and a 6 maybe the relevant and wanted target.
Alternatively, since the second consequence also includes that the character won’t choose to leave a combat prematurely, if one or both of the consequences aren’t resisted, you might as the GM simply take control of the Cutter like an NPC - or, differently, control them as a PC (since NPCs dont make rolls). If the Cutter is an NPC, you might treat them exactly like you would if a street fight attracted a nearby violent ghost - a battle becomes a 3-way fight between your Crew, the enemy, and the Cutter, with the Cutter imposing consequences or simply putting fictional things into play, e.g "Yan comes barreling at you and starts putting his knives into your gut over and over, his eyes wide, completely bloodshot. You’re taking the level 3 harm, ‘gutted’ " and let them resist those consequences - possibly guided by a Fortune Roll as above.
As a modification to the Fortune Roll, if you wanted to be nice, instead of 1 die you could roll the Cutter’s Resolve score in Fortune Dice and use those. But don’t forget to include the Cutter’s special abilities like “Not to be Trifled With” too when reciting consequences, even against the crew!
Hope that is helpful!