Mercenary patrol fleets raiding my pirate convoys

So I became friendly with the pirates and thus they send trade convoys to my colonies.

Now defending my colonies I have a mix of my own faction patrols and indepentent mercenary patrols. Those who belong to me leave the pirates alone and all is fine, but as you can guess the independents stop them dead in their track. As a result there is constantly a shortage of some good in my colonies and I'm sick of seing my fuel production plummet occationally as the volatiles, presumably mined on Garnir, gets plundered.

Is there anything I can do to get rid of these mercenaries. I've noticed in other runs that a greater military precence seems to replace the outsiders with fleets loyal to me, do I simply need to build more military bases?