! GLITCH WARNING !
Disclaimer: This happened to me so I'm speaking from personal experience. I've also read several threads online (ubi forums, x360a, reddit etc). Your experience may still be different.
During launch week many players experienced what is known as the echo bug/glitch. This glitch may occur during any of the missing persons side missions if/when your co-op partner interacts with an echo and progresses to the next part of the mission before you collect the echo yourself.
The echo will still appear on your map and you can interact with it, but after that part of the mission is completed the game fails to register it as "collected". This will lock you out of the corresponding achievement.
Solution: "You can solve this if you join another player and replay the quest in his lobby" (thanks NexusNiko). I'll elaborate: This may work if the session host has not done the mission himself and you're the first to activate the echo. For myself this eventually did work, although only after several collection attempts with different co-op hosts.
This glitch is not to be confused with inactive echoes that appear on your map but don't pop up in game. These are tied to missing persons side missions and become available during part X of a certain quest chain.
Some people myself included have encountered echoes whose markers get stuck on your map post collection. Don't worry though; as long as the numbers on the intel breakdown menu show that an area has been cleared, you're good to go.