Ah, this is a particular thing.
I had created a Mansard Like roof with the the multi-plane roof. However for elevation drawings for presentation, in order to reduce the amount of information we present to the board we flatten the top of the roof from a 2° or so pitch to a 0° pitch.
In order to do that, I have to break the roof up into single plane roofs since the scripting for the multi-plane roof cannot handle roof planes (at least in this configuration) that are 0°.
But roofs that have 0° slopes cannot ctrl click each other but do intersect with roof that have a >0° slope. I worked around it by changing the pitch temporarily, intersected the roofs that I needed to, and then changed the pitch back.