It happens when you load a game in a location where you've recruited a companion, and they have an item or effect which boosts stats. So if, for example, you load a game in Gilded Vale with Eder in your party and he has any items on which give a stat boost his stats will be permanently increased by that amount. Or if you load a game in Caed Nua with with Kana in your party. And that one is easy to see since he comes with a +1 intellect item on so you can save/load over and over in Caed Nua and watch his intellect go up.
Sensuki, how did you avoid it? As far as I know it happens every time you load a game in a couple major locations so unless you simply never saved the game there...