The marks are being caused by either the very hot iron reacting with the finishing chemicals if you haven't pre-washed, or any slight residue of soap if you have. It's really like a scorch, but will more than likely disappear when you wash it.
The best way to avoid this is by using a pressing cloth on 'lumpy' pieces - either a piece of thin muslin or a store bought one. I use a store bought one that is made up of some kind of mesh fabric so I can see what's underneath.
