I'm confused because dark and milk chocolate came up green, but they contain cocoa?

They certainly do and it's a valid question. However, with dark milk and milk chocolate, there is approximately between 5 - 50% cocoa powder in these. As such it has not hit the "intolerance threshold" of 100% and therefore your test was marked as green.

Meaning that when consuming cocoa powder it is best to consume it moderately to sparingly so as to not go over the threshold of 100% on a daily basis.

I.e milk chocolate would be fine moderately and dark chocolate sparingly. This is good to know when following a rotation diet.