Okay, so I dug around and found that there is actually
no difference in terms of friendly fire scoring modifiers across the different difficulty modes, so that would be unrelated. This means it's unlikely there's a bug here since we do have plenty of feedback and runs as far as Rogue mode goes.
It's likely more a question of play style. Destroying or
even just damaging allies can be extremely bad for your score if you do it at all frequently (especially depending on what you hit them with!) It's also possible you might feel more invincible and therefore reckless in a non-Rogue difficulty mode, leading to more collateral damage
Some of the negative score modifiers are pretty huge, and can stack up fast! With a scoresheet we could probably see more details, but I'm pretty sure that's it. Just stop shooting allies and your score will be much happier for it xD