Hey! That's difficult to test, so I can't confirm it yet, but I can see how that's potentially possible. Ideally Sims in relationships shouldn't be doing it, so yes, it's quite important this is not caused by the mod. I will look into it.
EDIT: After looking at autonomy tests, there's nothing in them that's directly affected by WonderfulWhims. There's a couple of reasons Sims can just flirt with others at random, but they are usually caused by the situation they are in.