Previously I tried equipping Mules with lots of Annihilator missile packs, which they promptly emptied into my engines.
If you could provide more detail about when/how that happens, that could be helpful in tracking this down. They're supposed to avoid friendly fire - and mostly do - so some specifics here would be really nice.
Most of my encounters with friendly fire happened with burst-style weapons or random-pattern weapons, the AI considers the initial firing sequence but if anything happens during, like the gun switching target to something else (due to R or target dying), it'll just spray over it. I've seen it /so/ often with Needlers as well as Annihilators, but it's very obvious with bombs since once they commit to the burst, that's what's happening. I don't have an example on hand, and the reasons vary, with Annihilators it's based on the fact that the AI seems to not consider 'what's behind/next' to the target that much, and given the spray of the weaponsystem, anything else it hits is collateral damage. I'm reasonably sure this can be tested with a mock gun that has a huge spray range cone, say 180 degrees, with friendlies in it, and a valid target, and the AI will probably just spam it no matter the collateral.