It's probably because the door is not centered in the doorway, both vertically and horizontally. Zoom in close and turn off snap sizing (the magnet button in the bottom left; make sure it is not depressed). Move your door so it fits the doorway exactly.
As for the boxes, it is likely the bottom of the box is underneath your ground plane. Raise it so it is a tiny bit above ground. Physics will take care of the rest
When I detail my maps, I almost always have entities that have physics placed noticeably above the floor/shelf/desk, etc which they are supposed to be on, so that they will fall into place. Good luck