I noticed the same thing with my Sportsman, with the old file. It seems to be because the file doesn't have the angled grind and thinness of the small blade to prevent it touching the main blade.
On my knife, the edge/lip of the file scratches against the blade, not the rough surface, which is lower than the flat lip surrounding it. I doubt that having the file facing out would make a difference.
It's a design flaw but hey, a few fine scratches on a blade are a tiny price to pay for having such a great knife. Keep enjoying it!
Is it one of the new nail files where the knurling goes all the way to the edge?
I'd like to know too, just for knowing's sake.
It's a little annoying but not really harmful. That's why Wenger reversed the file.
Look at the Evolution 10.
I haven't seen an Evolution 10. I do have a Traveller with the file facing in. The tip just touches the blade when I open it. I can't say if it's caused any scratches because the blade has fine scratches on both sides. Unlike on the Sportsman there's a significant gap between the blade and file when they're closed. The file is somewhat thinner than the Sportsman's.