You might have got some sand in there or something if they are very deep..... but I wouldn't worry about it one bit. They just look cooler the more you use em.
Think of it this way - did you buy it to be a wall mounted display piece, or did you buy it to actually chop stuff? If you bought it to chop stuff, go chop stuff with it!!!! I really don't understand the concern. Unless it looks like you took an angle grinder to it, I wouldn't worry. Are you that worried about a few wittle scratches on your big, bad chopper?!
And hey, go easy with the oil! If you want to avoid scratches, putting excess oil on your knife is the WORST thing you can do! A little oil is good - it protects against corrosion. Excessive amounts of oil traps dirt, grit, and dust, and as you are drawing your knife from the sheath it acts as an abrasive paste. (more scratches!~) A light coat is all you need. I keep an oiled rag in a Ziploc bag. Clean the blade first, wipe it with the rag, put the rag back in the bag so it won't dry out, done.
I use all of my knives. If I get ahold of something I don't use it gets sold or traded off. Scratches just come with the territory if you actually use your blades.