The DMT hones will leave scratches like that until they're broken in because there are high spots on the hone's surface. The best way to break it in is to use it. Howard rubs an old chisel on his new DMTs. I either hone a cheap kitchen knife for a while or do some strokes with pressure using a warped wedge razor that I have. It takes a little while to smooth things out, but after that it'll lap beautifully.

You might try using sandpaper to remove the scratches while your hone is breaking in.

Josh