When the opponent(s) have researched Insurgency, yet you are allied with them through Truce Among Rogues, they pile up in potentially quite significant quantities. I just played a game with 9 Vicious AIs, and one of my gravity wells had 13 neutral Kodiaks, as well as 10-15 each of several other types of neutral ships. This becomes problematic because researching Insurgency in this situation is completely counter productive, as those ships become a sizeable defensive force that you do not have to pay for (technically the opponent pays for it)

The only proposed solutions I would suggest are that 1) Insurgency does not affect players who have researched Truce Among Rogues or 2) An alternate neutral faction is created, one that is hostile regardless. This hostile faction could contain Vasari or Advent ships to add a little variety in the situation where Truce Among Rogues is in effect.