This just sounds like the Insurgency tech kicking in, not really any reason your ally should be immune to that, especially if it was some of the AI players that had researched it. Although I would agree that if an allied player was the one with Insurgency, it should not affect you (which may or may not be the case now, I have no idea)

Or just both play as TEC Rebels next time and make sure you research the TAR and Pirate Mercenaries techs at the same time so you don't have to be bothered with destroying those little Rebels...

That is a severely poor excuse. Moving on to the OP are you sure one of the enemy TEC did not research insurgency?

I think stardock needs to make some things clear with the TAR ability as i've been confused by some things as well.

If it is TEC-R vs TEC-R and both get TAR is neutrals and pirates useless that game? If so they should fix this by making the Neutrals around the planet owned by a player literally aligned with that player and his allies.

Kind of like what I said above if a TEC-R is allied with another player does his neutrals attack his allies.

If both players are TEC rebels local militia won't attack either of them, the pirate base becomes useless and neither faction can put up bounty (btw, even if I use carmic retribution to put bounty on the rebel won't be attacked. No problem with me, but if the pirates won't attack their allies when they have the most bounty on their heads WHY CAN'T I PUT UP BOUNTY FOR THEM THE NORMAL WAY? It's a great incentive in FFA games to have other players attack your neighbor instead of you).

What the OP experienced was one (more likely: multiple) TEC Loyalist(s) using Insurgents (tier 8 in the civilan research, at the end of the culture string). The TEC rebel pirate and milita reinforcements are NOT neutral, they belong to the TEC rebel player and only appear in the players gravitywells, not in the wells of allies.

You cannot help your friend with cleaning his gravitywells (because the Insurgents are neutral to you), and if you want to have an envoy of your friend in your gravitywell you will have to ask him to place a Starbase there, because the neutral insurgents on your planet WILL ATTACK HIS ENVOY.

TAR still needs fixing, they need to think about a solution for envoys, insurgents clogging up your planets and a problem others experienced where some neutral factions wouldn't be neutral at all. However the insurgent attacks on your friend are not TARs fault.

The ships that become under your direct control (those are the Pirate Mercs) will never attack your allies because they are converted to ships of your side, meaning the AI does not have any control over them so they are unable to attack your allies like all your other ships. Also, the rebel ships spawned by TAR won't appear in your allies' gravity wells. Only the insurgents will, even if they are spawned by your researched tech.

Truce Amongst Rogues.

As has been said, it's possible that an enemy TEC player researched Insurgency, which causes rebels to randomly stage revolts on enemy worlds.

Also I'm going to note I don't think I've ever experienced insurgents popping up on my worlds when TEC allies have had the tech in previous games, not sure about Rebellion.

While I dont have a lot of experience with pirate mercenaries, this does sound like Insurgency from an enemy TEC player.  As I understand, TEC rebels actually have to summon pirates now from the broadcast center.

While hangars do the trick, if your enemies have teched up that far, you and your ally should think about putting up starbases with auxiliary govt/enduring devotion on all of your planets in case they start building novaliths.  its expensive but you can take advantage of the trade expansions and Induced Reverence for Advent so that can help justify the cost.

Insurgency is researchable by TEC Loyalists as well as TEC Rebels, it's old tech, like, original Sins old.