The Doctor had to accept Donna's logic. Why block off an area that was seemingly not part of their plan?

"Humans!" the Doctor said. "You lot can't hear it, but you do have a tendency to stumble into trouble without meaning to." He gave Donna a pointed look, and then continued, "You hide a room, you put up barriers to keep out the alien life wandering around, yeah, but then when it comes down to it, a human could just as easily stumble in here. Hence, the dogs."

He turned around and peered into the darkness. "The question is, where are we?"