This. Just fix it Elite style: reset/relog and do the same thing again.
Works well for missions where you can easily check if everything matches up, but not so well if it could take a while, like in settlement massacre missions. That missing (or invisible/invincible) last NPC is always frustrating, and it seems to happen more often again. Fortunately I just do them for the kills these days, not for the mission reward.
This works for missing items in a box or locker, but for nothing else in systems that are in Thargoid recovery.
If the system is in Thargoid recovery and a settlement is not powered down, relogging won't help, as far as I know, nothing will. The only thing you can do is check the system map prior to taking the mission and see if the settlement has an X symbol above it on the map, if it doesn't, don't bother.
The Thargoid recovery system missions are borked. The first week they mission will be fine, the next tick, a large amount of settlements will be online and any missions that are listed
will be to a powered-up settlement. You will be hard pressed to find
any missions to an offline settlement even though they exist. After the first week of thargoid recovery I don't bother with the systems, it's too painful, after reaching friendly status with the local groups, to sit there and scan the mission list of up to 30 missions and none will be offline. Even worse, rewards like manufacturing instructions will be raining down and the settlements will all be online.
Other missions like "fetch an item from x person at x settlement" and "deliver x item to x person at x settlement", or "get x item from x settlement", the person or item will not spawn. You can relog, you fly off and reset the instance, nothing works. I even left one fetch an item mission, did other missions while I called over a small ship so I could land at the pad and use the ships station menu to verify that didn't have to be used to acquire the item. Nothing worked.
This is really starting to kill my buzz about this game, I need like
80 manufacturing instructions to complete the mods I need to upgrade just 2 suits and 2 weapons to G5
from G4. I not only feel burned by this excessive requirement for manufacturing instructions, that inexplicably need to be on both suit and weapon upgrades, but the fact they are available only on missions for stations that are online.
The other thing that kills my buzz is the fact that this has been reported and crickets is all you hear. This is part of the big feature war going on and it's not being fixed.
Last night I left the system I was at and looked around in neighboring systems for restore missions and ended up leaving the area. Nothing, zip, nada. Oh, there were tons of missions to online power plants and manufacturing instruction as well power supplies were dropping like candy from a birthday pinata. I finally went to a couple of systems that were in famine or bust and there were missions, they paid nothing and the mat rewards were for crap that I have 40 or 50 of. I have everything I need but power supplies and manufacturing instructions to do all the engineering that I want to do. Oh, except for opinion polls and settlement defense plans. I've done well over 125 restore missions and have gotten just 2 settlement defense plans and maybe 5 opinion polls.
It's starting to be that the only reason I want to play the game is the fact that I just spent a ton of money upgrading my joysticks and rudder pedals. It's really starting to rub me the wrong way. Maybe it's time to take another year off and do other things, except the fact that these issues will likely still need to be addressed when I come back. For now, the thargoid war can go to a very hot place and reside there permanently.
it’s like to had an flat tire and the company wouldn’t change it or repair it on their behalf so you must do it by yourself. 
