The storms didn't let them explore that much. We also don't know how long they traveled to the necropolis.
They didn't explore that much, from what we could see. They rushed through the storm and landed in a place suitable for landing, close to the origin of the signal.
They were not that concerned with exploring the overall terrain (they could do so later), but more on where the signal was coming from.
Finally, after David rescued them, they might have moved for a long time (possible hours) before reaching the necropolis. That would imply a large distance (some miles) which may have hidden the city from the landing craft (due to the surrounding mountain range).
You can also consider this a plot hole...