The bug that
@Brandon Gill is talking about was introduced with the Twilight pack. They changed something and since then when placing one of the premade habitat blueprints, the terrain is raised (even if you perfectly adjust the blueprint to the ground level) and it makes a kind of a pit around the habitat. The habitat door appears sunken on the ground and you cannot connect a path, so the habitat is invalid. In addition, you can't modify the terrain that has been deformed around the habitat because it is obstructed by barrier. Therefore, the solution is deleting the blueprint barriers, fixing the terrain yourself and placing new barriers again. The main purpose for the premade habitat blueprints is that people who don't like building or don't have good skills to build a habitat themselves can play the game. If Frontier includes blueprints but they cannot be used, it should be fixed. I reported the issue back then for Brandon:
https://issues.frontierstore.net/issue-detail/55358
It would be nice if other people would contribute to the issue even if this bug doesn't bother them. Meanwhile, the only thing we can do is waiting until Frontier fixes the bug in a future update.