How about some more detail? Things like water quality, Ammonia, Nitrates, Nitrites, PH, water temp. etc...also a pic might help.
How long have you noticed the spots.? Also, you said you have clowns in the same tank. The loach police will be by to tell you that is not a good mix soon

since dojos are cold water species and clowns are definitely tropical and there is about a 10 degree difference in what they need to thrive. Dojos need a temp of 50- 68ºF (10 - 20ºC). You can find more info in the species index. Clowns need 78ºF to 83ºF and if you try to reach a medium neither one is going to be comfortable.
Also, people don't realize that as the dojos grow they shed their skin sometimes...and right before they shed they tend to look a little ragged and it can look like they are diseased. It freaked me out the first time I saw the skin floating in my tank. I have 5 dojos in a coldwater tank and as they get fatter and longer they shed.
Hope this helps...
Kevin