Use more missiles. All of them.*Our own PDs don't shoot down our own missiles - where did you get that idea? No, what I am saying is that if there are 5 NPCs in close proximity, and I fire at an enemy who doesn't have a PD, one of the "bystander" NPCs will shoot down my missiles. This should not happen, nor can I do anything about it except give up using missiles (which is a shame, because I like missiles).
*requires pack-hounds.