Since there are so many ways to create a colored ellipse it might be helpful to know which method you chose, masked solid, shape layer, circle effect?
How was it colored? Fill, effect, gradient…? Did you move all attributes to the new composition when you precomped?
My guess is whatever method you chose broke the render order.
I’ll invoke Brian Maffit’s exhortation to remember M E T, Masks, Effects then Transformations. That’s the order you need to respect when nesting comps.