This affects KDF only. I've seen the Sector maps with my Stafleet characters, and the star systems with mission objectives are not opaque.
When I open up my map (press "M"), the systems that advance missions (i.e. DS9 for "Second Wave") are opaque. It's a giant yellowish blob. I can click on the systems inside the blobs, but that's half memory & half trial/error... like getting to Bajor when the DS9 area is yellow blobbed out.
This is another KDF visual annoyance only (no Starfleet equivalent, like the Marauder/Diplomacy Doff thing, where the KDF side is bugged), so I guess it won't be fixed... but this has been the case for me since Season 6.