Black Box missions, any kind of surface scan missions or having to destroy power on a base, and illegal Black Box missions, and war conflict zones are what I mainly have been seeing.
For all of them the missions will either not let you complete them, during the reward it will actually show you a red bar instead of green for influence, and war makes no sense. Sometimes it is normal and when I fight it shows victory, other times I have to not fight and it will bring victory.