I went for ultrasound ytd and the Dr said my 12 weeks old baby is very deep inside.

That sounds a bit worrying to hear, but try not to panic just yet as baby positions can vary quite a bit at 12 weeks. It might be worth calling your gynae back to ask them to explain what they meant exactly, whether it affects anything for now, and what to monitor going forward, just so you have a clearer picture. Some gynae clinics are quite open to a quick phone consult to put your mind at ease, and if you feel unsure about the answer you get, a second opinion is always an option too.