For example, with the Paladin's Divine Grace, the wording says "bonus, if any", which suggests that a penalty wouldn't be applied. However, HeroLab does apply it.
In the case of Divine Grace, you don't take a penalty to saving throws if your Charisma drops below 10. Feeblemind does attack Wisdom, however, which comes with a lowering of Will saves. If HeroLabs applied Divine Grace as a penalty, then it's an error in their coding.