Battle of pharsalus was a civil war battle between caesar and pompey.
Would it not have been extremely confusing once the lines of legions clashed for them to make distinctions on who they should kill?
This is obviously a reoccurring issue throughout history, wondering if there was a color protocol or something enacted by both sides before combat took place?
As you also mentioned an interest in broader historical "Friend or Foe" identification, although it doesn't really touch on the Civil War, which of course presented more specific problems, /u/papiriuscursor does discuss the issue for the Romans in this previous thread, which would likely interest you.