removing scratches from black walnut with a BLO finish

You  can sand out the scratches you missed before applying the oil.  You should use a sanding block and sand a large enough area that you avoid sanding in "dips" where the scratches were.  In future a close inspection, using light from a low side angle is a good thing.  The wood can be wet with mineral spirits or naphtha to help reveal defects. 

I doubt you will see much difference in the sanded portions when you reapply another coat of BLO--your last.  (One coat of BLO is all that is desirable.)  BLO by itself is just for wetting out the wood to help reveal grain.  Otherwise it makes a lousy finish since it offers almost no protection against water spotting or other defects.  It also "ages" quickly, calling for frequent repair.  A much better alternative to using BLO by itself is to mix BLO with varnish thinned with mineral spirits.  The oil varnish mix gives much more protection, and in a couple of coats gives virtually the same look that BLO by itself would have.  It will require much less frequent refreshing and will protect much better against water spotting.  Frankly, in most cases you might as well start with the oil/varnish mix--it will bring out grain just about identically to starting with an initial oil coat. 

You may be seeing chatoyance where the wood shows different tones from different angles.  That's a natural property--you really can't eliminate it, unless you essentially mask the wood, but it best work you should be aware of it when selecting wood so that an attractive and consistant pattern.  You may also be seeing different absorbancy of the oill if it weren't applied evenly.  That will disappear with subsequent coats.