XXVINTAGEXX, It is often either her hymen that is fully blocking her vaginal opening or labial adhesions.
Labial adhesions is fairly common (as many as 1% of young girls). Her labia is sticking to each other and growing together. It is caused by low estrogen levels and rubbing an estrogen cream onto it will separate it again.
If she has an imperforate hymen (no hole), you will have to monitor it when she gets to puberty. If it does not open up by itself, it will have to be surgically cut in order for her first menstrual period to get out.
There are also conditions where a girl will not have a vagina. I do however think that the doctor would have told you if that were the case.
Speak to your doctor again. Find out exactly why this happened and what you can do about it.
Take care!