[Nyctaeus]

Aaah, the memories return.

So... So far in M02,

Spoiler:

my wingmates return to the TAGged pirate convoy to destroy it. And I have no way to stop them because I cannot issue orders

. Mission is not beatable without cheats I guess.

That shouldn't be possible. I tested that mission dozens of times and never had that happened. Tagged ships get protected, the AI shouldn't attack them.

Are you talking return back AFTER pulling away?

Ye, we pretend to disengage and when our wingmates reach the waypoint like 5 clicks from the convoy, they immediately turn back and burn hard to kill the TAGged freighters.

[TrashMan]

This is odd. Checking the mission in FRED, when a a ship is tagged it's protected. The protection is never removed.
And when 70% of the convoy is destroyed, Alpha and Beta are given order to go to waypoint (no clearing of previous orders).
They shouldn't go after them.

In my testing I usually waited before tagging, so the convoy departed, but I never noticed the wingmen attacking them in any of my test playtroughs. Hmm.....

EDIT: This should fix it. Specifically ordered ships to play dead.