After converting voxels to elements, Cubik is creating a palette and assign each element to a color in that palette.
Paint tool is actually modifying the texture pixels where you clicked on the surface. So if you use pen pain tool and left click on a red surface, the palette will change the red to something else and so all elements with UV pointing there will also change color.
To avoid that, you need to ask Cubik to recalculate a new texture and UVs (this is an advanced function with expert behavior). To do so, go to Material Manager (where textures are listed), click "..." button and select "Create atlas, keep textures". By doing so, Cubik will create a new texture containing unique zones for each face of each element. Bringing you a way to paint safely on your model.
This feature is one of the most advanced Cubik Studio has and is currently probably my favorite one.