i.e. courier missions, liberation stuff, assassination contracts. I'm assuming these won't all become unavailable once I finish the story right? or am i wrong and should finish all of these while I am still progressing through the story? I'm on sequence 8 right now.
I seriously doubt there will be a patch for the "missing" quest icons. They're missing because you haven't found them yet. Icons just don't show up in areas you've not explored. Sure its a pain if the quest is in a single foggy pixel in an otherwise explored area but its the way it is. I for one am glad they did it this way. Otherwise it would be like any other sandbox game where you just run run icon to icon with no real need to explore.