What causes extremely low vitamin d and vitamin b12 folate?

Vitamins: Vitamin d comes from the sun, and fortified milk and other foods. Iceland had a high incidence of rickets years ago due to poor sunlight. B12 and folate are obtained through foods, B12 from meat and other animal proteins. You can search the list. B12 may be problematic if you can't absorb it in your diet- pernicious anemia is a disease that prevents absorption. Poor nutrition -> low b12/folate.

Depends: Sometimes it can be malabsorption, which can be due to gluten sensitivity. Gluten beats up the gut cells and the gut, and decreases the ability to absorb certain things. Commonly we see such people low in d, B12 and iron as well as magnesium and zinc.