Honestly, if there's one thing I have to hand to this game (frustrating though it may be), it's that every infuriating thing that happens to my pawns IS usually my fault. Friendly fire is one of those. I can't think of a single instance of friendly fire that didn't occur because I forgot to undraft a guy, or didn't micro a grenade/molotov thrower properly.
Yeah, it's frustrating, but this game is incredibly straight forward and intuitive about its AI processes (which is more than I can say for a lot of games - I have no clue what went wrong half the time in Castle Story or Banished). If pawns aren't acting how you want, it's always because YOU restricted the wrong thing, didn't prioritize your zones properly, forgot to toggle a switch or (in this case) didn't do a good job of positioning them in the fight and microing their drafts.
PS: In real life, it actually makes a ton of sense for civilian pawns (and most of your pawns have civilian backstories) to friendly fire each other if they're in the same equivalent line of fire, especially under high stress or when wounded. Yeah, friendly fire should be rolled less often the more skilled a shooter your pawn is, but as far as I know this is already in play.