There is actually an explanation for why Cortana’s line is out of place.
The line, “this cave is not a natural formation” was admitted by Bungie to be a somewhat useless line due to its obviousness. Originally, the cave in question was meant to look natural, and the line was meant to indicate that only Cortana could tell that it was artificial. However, the developers didn’t want to spend time creating all the geometry for the tunnel, so they ended up keeping the tunnel in a blocky Forerunner style. Despite this, Cortana’s line was never removed. (source)