There are two possible issues here. If you are starting with RGB data, it is difficult to determine an RGB combination that will generate exactly 100% or 0% of the primary and secondary CMY colours. It is also possible that the gamut of the printer is larger than the RGB you are using in this area. (This is not unusual for some RGB colour spaces and you could try defining your RGB as a larger gamut RGB, such as Adobe RGB). To get around the problem you can edit one (or both) of the profiles.
If you are starting with CMYK data and using colour management to transform it for another CMYK, this can result in pure colours in the original CMYK being "contaminated" by small amounts of another ink. This is a particular problem for spot colours and arises because of a small difference in colour between the two ink sets and is a result of the colour management attempting to produce the correct hue. For many production situations such a result can be a problem as it can give rise to unpleasant halftoning artefacts on some proofing devices and for traditional printing produces colours in which unwanted variations may arise during the run. If you wish to avoid this, it is again necessary to edit the profiles to achieve it.
Color managed workflows using ICC profiles often suffer from this problem. Most ICC profiles are built with settings for GCR, or gray component replacement.GCR takes a certain amount of gray component colors (C+M+Y combined) and replaces it with black ink. If a too-strong GCR level is used, or the black start point is set too low, you will see tiny black dots contaminating your colors.
Fortunately, it is possible in Wasatch SoftRIP to manually override the managed ICC workflow and use a percentage of the device's raw channels to output spot colors. This is most useful, for example, when you want to replace a mixed black ink with 100% of your black ink and no additional colors. Please refer to the Wasatch Help files (available from the Help menu, under Help Subjects > Wasatch SoftRIP > Color Controls > Special Colors) for more information about this process.