What are the most common reasons for Vitamin D deficiency even after taking supplements for 3 months?
It all depends how deficient you were - they MEASURE blood levels but vit D is stored in the body and the low level in the blood is no indication of how low the stores are. If you were very low then it will need more vit D supplements to replenish them.
And of course it also depends on how much vit D was in your supplement - the usual amounts you buy OTC could take years to do it if they could at all. You need some time at a high dose. The UK recommendation is to start with 8-10 weeks at 60,000 IU per week either as a single dose or 3x20,000IU. Other places say that a longer period with a lower dose is better and you are more likely to absorb it - say 25,000 IU per week over 4 months. But that is still a fair amount. And then there MAY be a malabsorption problem if you are taking oral vit D.