The stability of the wax is one reason these so called contaminants are removed. Additionally they dilute the concentration of the pigment added to give encaustic its color. In combination with a hardener (damar, carnauba, etcetera) and a pigment, the wax can not hold the addition of the contaminant without losing its ability to stay structurally stable. Consider the contaminate in the ratios when choosing to use crude or unrefined beeswax to prevent such problems. However, these ratios can be difficult to gauge and it is suggested that you only use a very small percentage of pigment. The recipe should include the contaminate as part of the combined collection of pigments that make up the necessary percentage. And when making your own concentrated encaustic colors use pharmaceutical grade beeswax. This is particularly important when making white encaustic paints.
To learn more on making your own encaustic paint read How to Make Encaustic Medium and Paint.