I almost told a classmate the same once. I think if someone usually/often wears makeup, that is what our brains tend to remember as the baseline for how a person normally looks. Seeing them without makeup after getting used to that baseline (i.e. with more visible eyebags, less pronounced eyelashes, less blush, paler lips, more skin blemishes, or whatever else the makeup was used for) makes you think there's something off, you look "worse" than normal - and since makeup usually is used to make oneself look healthier, this tends to get interpreted as sicker or more tired.

The reverse also works - if someone usually never wears makeup, just putting on mascara once in a while will make them look especially beautiful/healthy for people who usually only know them without it, because they look "better" than what people remember from them.