Well I imagine our Spymaster, Commander (and even our Diplomat) have ruffled more than a few feathers over time. There could be a number of unintended consequences from our actions. MIke mentions Ferelden being angry that we had taken over a keep in their lands (Crestwood) and stationed forces there. The flipside being, did you want bandits to have it?
I have a feeling that we may be eroding the stability of these nations as we have made them look inept in the handling of the recent crises (and dependent on us). As more flock to our banner, there's probably all sorts of power struggles (and subsequent collateral damage) happening behind the scenes.
Also, if you are in charge of an organization as big as the Inquisition, you cannot keep an eye out on all your people all the time. Some will go behind your back and misuse the resources allocated or use their position just to further their own goals, perhaps even in less savory manner. But this has me thinking that maybe it could link to some of the judgment calls you made? For example, if you recruited someone like, say, Florianne, as an agent, she only played nice for a bit, then decided to do her own awful thing while hiding behind the Inquisition banner?
Re Crestwood - my thoughts exactly