I iron from the back because of this sort of thing. Typically I use a hot iron and steam and sometimes get the shiny stuff, which has always gone away after washing from me.
If it is distressing you, try adding a towel to cushion your ironing board first. You can also try a wooden dowel (can typically buy at your local hardware store). I'd try something about half an inch or smaller diameter. Put the dowel down on your ironing board and position the seam over it, then when you press you are only getting the seam.