From the Player's Basic Rules, page 36 (the section on Backgrounds):
Each background gives a character proficiency in two skills. Skills are described in chapter 7. In addition, most backgrounds give a character proficiency with one or more tools. Tools and tool proficiencies are detailed in chapter 5. If a character would gain the same proficiency from two different sources, he or she can choose a different proficiency of the same kind (skill or tool) instead.
So in this situation, where you receive proficiency with the disguise kit from 2 different sources, you simply choose another tool to gain proficiency in. Note that this has to be a tool proficiency, not a skill proficiency.