I know this thread is 5 years old now but this rely is for anybody looking for help now like me.
Had this problem just now. I put it in edit mode (CTRL + E) went to spawn point 45 and couldn't see anything. Went over to that point and the contact was there but was glitched inside the wall (I could only see his shield on his back) but I could still talk to him.
This might be what is going on with missing contacts and bounties on the game. They are spawning inside the buildings. Perhaps the game developers originally planned to allow you to go inside buildings in villages but changed their minds, resulting in this bug.
