Sorry... but facility scrapping??

It's under cargo options. Weird and confusing, but that's where they put it.

Go to your colony list. Click on a colony. Click the 'Scrap Cargo' button. When the window opens up showing you everything on the colony, scroll down past what you would normally think of as cargo such as units until you get to the facilities.

That is absolutely crazy to put it there. Maybe call it something other then scrap cargo, I just didn't scrap facilitys until I read on the forum where it was.

Yeah, that's pretty odd. They really should have stuck it under the extended yard options, in my opinion, over where things like scrapping, mothballing, and retrofitting starships are stashed.