If you haven’t started this quest yet, go talk to the Majordomo in Prodromos (you must have completed the quest "Task: Naming the Dead") and exhaust his dialogue options. If those conditions are met, he should point out a difference in the number of lost colonists compared to the numbers of dead you reported, and encourages you to look into the discrepancy.
Fast-travel back to Site 1 and set the quest "Doesn’t Add Up" as your active quest and note there are four "muster sites" for you to search. One is southwest of Site 1, up the large hill leading to the first monolith. Head to the indicated site to find a beacon, then scan a "Shuttle burn mark" on the ground - it won’t highlight, so just aim for the black marks and scan.
The second muster site is southeast of the Site 1 Forward Station, on the hill where you found Lito’s Datapad. Scan the "Shuttle burn mark" here, then head off to Site 2. From Site 2 continue southwest to find another muster site near the lake. Do your scanning, listen to SAM whine for more data, then return to Site 2 and head east into the desert to find the fourth muster point.
If you come here before advancing "A Trail of Hope" this muster point will be in a level 3 radiation hazard, which you can technically still scan by driving close with the Nomad, popping out, scanning, then quickly diving into the Nomad for shelter… but you may as well wait a bit so the radiation will be gone. Scan the "Shuttle burn mark" and SAM will finally have enough info to point you to where the shuttles may have gone.
Return to the Tempest and plot a course for the Eriksson system, where you’ll now be able to scan for a new anomaly, an "Eezo-Distorted Kett Wreckage". Plunder the wreckage for some salvage, then scan the system again to find a "Drifting Initiative Shuttle". Visiting this ship will complete the quest, earning you XP and 29 AVP, after which you can harvest some salvage from the drifting shuttle.