Hi, Toby,
As you have found, it can be problematic using the Blue/Green Screen effect when the image contains both blue and green.
You can isolate one of the colors by placing the playhead over the frame the dominant color that you want to isolate before you choose the Blue/Green screen effect. Here's an excerpt from the Apple online help menu re the Green Screen feature:
"The color that iMovie removes is based on the dominant color in the frame at the position of the playhead
when you choose Green/Blue Screen from the pop-up menu. If the frame below the playhead isn’t representative of the rest of the clip, you may need to reposition the playhead and reapply the effect."
So, you might try tinkering with the above method to see if you can get the effect that you want. Here's the link to the full Green Screen help menu item:
https://help.apple.com/imovie/mac/10.1/#/mov82da1338a
-- Rich