My baby is 13 going on 14 months. I noticed about a week ago that at night she will start to cry and will go back to sleep if I pat her etc and she does this about 3 times or so at different times during the night. She did not use to do this before, but I noticed it was after she got her 3shots for MMR etc and I know that she is getting molars on the top and bottom also. I am just concerned that there may be something else wrong, or if the shots and molars may have something to do with it?

Most likely the molars have something to do with this behavior. However, as children grow, their sleep patterns tend to change before settling into a permanent routine. Just keep doing as you are doing and this shall pass.