As soon as I finish the factory and the multiblock forms, the factory creates a shell of barrier blocks around the basic tier 1 shape, which if making a tier 1 factory also removes the cap stones. It makes it impossible to add totems after the fact, or even operate a basic factory. Any ideas what is causing this????

Nevermind, I misunderstood the need of the 'clear space' and made my factory there, which is where I assume the factory utilizes space to 'learn' the mob. I Am Dumb.