Your sewing machine probably does not feed the upper and lower layers evenly.
Have you tried glue basting? I do this on the ironing board. Take a pin straight down through the two seams and into the ironing board. Place a tiny dot of Elmer's washable school glue (white glue) inside the seam allowance. Use hot iron on the seam for a few seconds to set the glue. Remove pin. Glue secures the seam for me better than a pin does.
When you take the pieces to the sewing machine, pay attention as you sew and see if the presser foot is pushing the top fabric into the seam. If it is, you will see a little ripple on top as you come to the glue. On some machines you can adjust the presser foot pressure to lighten it up. This is also why some people use a walking foot while piecing -- to make sure the two layers are feeding evenly.