Sneaky girls, aren't they? I would go with Turtle's advice, raise their roost. My hens are weird though. Some like it high and some even nest in the low nesting boxes.
What about cutting the sides of the carton down? There isn't a lot of Height room in the coop and if i raise it to much more they will be within pecking range of the rope lights and other power stuff.
You could try cutting it down to just hold in the hay. That may do the trick. And the jagged pattern from the crate will feel weird on their feet and may discourage roosting on it.