Yeah the AI for sure have a tendency to gain up on "strongest" player, which is usually the human player. Though others have said they still have preference for targetting humans, perhaps because they can at least understand the other AI's diplomatic system.
Put simply, diplomacy has always been one of Sins weak points, which is why they are doing an expansion on it. Either do what Haree said and always play on locked teams or do every single mission you get, its really all you can do.
