Anyone know how to get them to work with mission objectives? I read in several places that they can be used for that but I can only get it to work with anomolies.
There's nothing special you have to do, it's more coincidental. Anything in the ground game that's 'flashy', (computer consoles, crates, etc.) can be scanned down, as well as anomalies. In space, sometimes the scanner will point you toward scanning objectives (asteroids, installations, etc.), other times it won't. Good luck!