Hi BrettL,
the colored dots besides the Alternatives indicate the level of changes undertaken in the Alternative with respect to the parent Alternative. Within that, green means no changes, blue means changes of attributes (like manhole diameter), yellow means new elements added and red means elements deleted. The order of the colors is green, blue, yellow, red. That means when you delete an element and change another the color will be red, always indicating the changes with highest order.
Best Regards
Ralf