No bug, you just didn't read the fine print on the extractor and the tiny drill manufacture project. The project alone takes 30 space before you can start adding runts, so you need at least one extra manufacturing building to finish the project. And don't cancel the project or you'll lose your tiny drill and menacing hull. I'd suggest loading a save before you started the project if you have one and waiting until you have more workspace, or building a second extractor ASAP.