I've noticed a difference in the behaviors of convoys I'm "escorting" when they get a different jump point than I do. Normally, when we undock from the station to begin the trip, we are all assigned the same jump point. In this case, as long as I'm a member of the group I can kill up to two members of the convoy within the station sector with no penalty other than aggroing the turrets when I start shooting, and then aggroing the NPC escorts after the second death (along with being kicked out of the mission at that point). There is no faction penalty and the yellow warning text doesn't appear.

If, however, they are assigned a different jump point than I am, then when I attack them I get the yellow "this ship is under our protection" notice, and when I kill it I get the faction penalty, despite being in their group.

Hopefully this will offer some clue as to what part of the codebase is responsible for the differing jump point bug.

Huh, that's an interesting bit of info. Thanks!