There are certain areas the mod won't cover. I don't know why it isn't touching them. I had had 2 separate networks, one using stone brick, and one using refined concrete. Eventually my factory expanded to consume that outpost, but the stone brick wouldn't upgrade. I deconstructed the stone brick, but now it's just leaving that area uncovered.

Bump since this is still a problem

Have you installed or uninstalled any mods that add types of ground covering, like Dectorio?

Nope. I've never used them.