People taking levothyroxine frequently remain too low in the range for the biologically active thyroid hormones Free T4 and Free T3. Even when the dose is high enough to raise Free T4 to the top of its range, frequently the Free T3 will remain too low in its range to relieve symptoms.
When hypothyroid the patient often does not produce adequate stomach acid to absorb vitamins and nutrients well. The result is low Vitamin D, B12 and ferritin (iron). So the low vitamins/minerals don't cause the problem with taking thyroid med, the hypothyroidism causes problems absorbing enough vitamins/minerals.
Just because your thyroid test results were within their reference range doesn't mean they are optimal. Please post your test results and reference ranges shown on the lab report. Also please tell us about any symptoms you have.
Don't believe that is a problem. The lack of vitamins/minerals actually might be due to a lack of stomach acid due to still being hypothyroid. Perhaps we could better answer your questions if you will post your thyroid related test results and reference ranges shown on the lab report. Also, please tell us about any symptoms you have. And please post the test results for any vitamins/minerals that have shown to be low.