Normally more noticable on a Kohaku that was otherwise unblemished - Some little black spots appear these are called Shimi, but should not be confused with that particular koi suddenly producing a definite black pigment which develops into a definite black spot .. these may be more permanent
This is an unfortunate genetic defect in some fish such as a Kohaku when it gets some little black dots and they're suddenly a Sanke. 

There is also many now that believe that these small black spots, or shimi's may be caused by the actual water conditions such as a high turnover rate or to an exposure to caustic irritants such as Chlorine, which of course is now contained in our everyday tap water - thus it is even more important that the water entering our pond and tank systems is fed through a water purification unit that does remove traces of Chlorine and other impurities. Why do we believe this could cause these Shimi's ? Well it is rarely noted that in natural green water ponds these Shimi's are much less frequent, if ever .... so there may be something in trying to provide green water at a level that we can still view our prized possessions.

Another condition that can cause black spots to appear is a type the black appears on the fins and body and this could be caused by sudden stress levels or from some pond water treatment that did not suit that particular fish ... For example: Fish that may be badly ammonia burned by a filtration failure or simply not sufficient filtration and this can cause these blackened areas and is called 'Melanophore Migration'. Severe parasitic attack can later cause such blackening of the skin but as the skin starts to heal then the blackening may start to disappear and may not permanent, but may take two to four weeks before showing any real signs of improvement.

Shimi's can be removed - but this should be done by someone who has knowledge of using anaesthetics and is used to treating fish ..  the process is that the koi is anaesthetised and then once the fish is calm and will not flap about on the top of a bench or table covered with a damp cloth, then the shimi can very carefully be scraped away using a sharp scalpel ...if it is a true shimi then it is like black ink just under the mucus layer and will come away quite easily .... once the shimi has been removed I suggest that you place a dab of topical dressing on that area to prevent a secondary infection from setting in .... prevention is of course better than a cure ...