@teekayy Those marks are from when you lift the film on the second stage of install and it folds or comes to point when you lift it.
On your second stage(the lift and tuck) make sure you bend the film in such a way as not to make it come to point during the lift. Make your fingers long and angled. You also might want to try not going down so far on the first stage of install. This will allow more room for the lift and tuck on the second stage and might stop those marks because the film has more room to move without coming to a point.
And as @drtint4211 said,, be careful when you pull the liner on the second stage. If it comes to a point when you pull it, instead of it coming off smooth and even,,, then it will cause the marks also. Usually though, when this happens it is more of a "zipper" looking mark, like drtint4211 said.
Also == At the end of your install when doing a check of the window.... if you will hit those spots carefully with a heat gun and a lil' chisler as soon as you seen them, they will all but go away and lay down just fine. Just be quick and don't scratch the film when you do this.