Can liver problems cause low levels of vitamin d and vitamin b12?

Yes, but other: causes are more common. You may not taking enough of these vitamins with your diet. Try taking 5000 units of vitamin D3 daily for three months and retest. B12 is more complicated, if you have poor absorption you will need injection of B12. For now try taking about 50 micrograms of B12 daily by mouth and recheck in about 3 months.