There are many things that could be the cause of the pains that your girlfriend is experiencing. If the pills that the doctor prescribed are not helping then she should go back to the doctor. If she is worried that the doctor she has been visiting is not helping, you can always go and get a second opinion, which I strongly suggest. They may be able to perform further tests to find out what is happening, it is possible that the birth control shot is not even the cause of the problem, although if she does see a second doctor she should tell him everything that has been going on. It is very wise to get a second opinion if the first doctor you see doesn’t seem to be helping.
Good luck.