The simple view of the bonding in methane You will be familiar with drawing methane using dots and crosses diagrams, but it is worth looking at its structure a bit more closely. There is a serious mis-match between this structure and the modern electronic structure of carbon, 1s 2 2s 2 2p x 1 2p y 1.
Lack of sun exposure: Lack of sun exposure is a major cause of low vitamin d level especially if you live in the northern us. Less likely would be lack of vitamin d in food, but also a possibility if you are on a very restrictive diet.
But many people who avoid meat don't become deficient in vitamin B12. Many other foods, especially fish, contain vitamin B12. There are a couple of diseases that could cause low levels of vitamins D and B12. Celiac disease (gluten sensitivity) might cause vitamin and mineral deficiencies without specific symptoms. Crohn's disease could also cause both, but most people with Crohn's will have symptoms such as abdominal pain and frequent stools.