Based on the description that you are giving, it sounds like your daughter has the type of birth mark known as a macular stain. These are small malformations in the tiny blood vessels, called capillaries, under the skin, and they are extremely common. In common language, they are variably known as 'stork bites', 'salmon patches', or 'angel kisses.' Because these macular stains are composed of blood vessels, they are sensitive to thing that increase blood flow. In a young child, these most typically would be crying or other types of emotion; therefore, it is very common and totally normal to have these spots look darker at these times.
If you have not talked to your pediatrician
or pediatric dermatologist
about this issue, I would still recommend that you do so. First of all, to confirm that this is indeed just a macular stain and not another form of birthmark. Second, because most of the time macular stains are beginning to fade after the first 1 or 2 years of life. If the stain is still strongly present at 3 years of age, then this might be a sign that it is going to persist for years. If so, depending on the size or location, it might be a cosmetic problem and you might want to discuss treatment options with your pediatrician or pediatric dermatologist.