I had one where the last scav was no where to be found (drove around in an SRV with the contacts panel open, was a smaller settlement too so should have seen them show up in the list). Fixed it by relogging inside the settlement. My theory is that they must have spawned under ground and fell to the center of the planet (putting them far out of reach of the contacts panel). Whether you super cruise in or log in seems to impact location/placements of things (boxes, people).
Yes, this is usualy what happens with "missing" scavs. Sometimes, on certain settlements, they can spawn embedded into ground by half of thier bodies (this can vary how much they bury into ground), and if they move, or go into "attack" stance, it can cause them to fall, but it can also "unplug" them from ground. Thats why sometimes few attempts are needed.
To fix its very simple... reseting instance will do. Best done by re-enter supercruz, and drop back... as relogging instead of this, will cause all loot to be gone, its mechanic to prevent material farming by reloggin. But if one dont plan loot, wanting just kill scavs, relogging might be faster solution to this.
Have yet to had mission like this wich had "missing" scavs, that would reseting instance once or twice did not help. And its usually is when I pick a 10 manufactured instructions reward mission from npcs after hardest negotiate as succesfull.
But some folks who taken voice here are unpatient, and they will rather waste thier time complain how ED:0dd is bad and broken, here on forums on every possible chance, while they could still finish thier mission regadless, but they didnt, as they have no idea how game works... How silly of them, but reading thier stories gives me a laugh every time I see it.