To “sit uncomfortably with” means to hold onto a thought and/ or emotion that makes you feel some sort of negative, sad, scary, uneasy or confusing emotion/s for an extended amount of time. It is a variation on “sit with”, which means to think over or think about something and see how it makes you feel. Imagine if the thing that you have to “sit uncomfortably with” was a meal that was working its way through your body.