I hope I'm not stating the obvious but from what I've experienced in 1.3, if your relations are under 0 and they are outraged, they will start to join coalitions. If you increase relations to over +50, they start to leave the coalition. These changes are not always instant, as it depends whether they are at peace/war, their strength/loans?, whether they have a diplomat spare to join/leave etc.
I'm not sure if they join at threatened, and if they do, maybe its at a different relation value? e.g. under 0 or under -50?
Use your diplomats to get enemies out of coalitions, or better still, keep your relations with them above 0 (factor in the AE hit to come) to prevent them joining coalitions.
And hope like hell that your not the only country with AE against you.