I just completed "Patrol the Elwing System" (part of "Patrol the Cardassia Sector") and was awarded for completing the Patrol Mission as well as my "Explore Strange New Worlds" mission. I don't know if this is a big issue but if I'm reading the mission correctly, I should only be receiving credit towards "Explore Strange New Worlds" by completing missions in Star Clusters, not through normal sector patrols.
I believe "Explore Strange New Worlds" was at 2/3 from doing actual Star Cluster missions before I started the normal patrol mission.
I've noticed that on the Fed side that mission awards the ore after only one exploration instead of after you complete 3 as in the mission description.
On the Klingon side the comparable mission doesn't award Ore until you've completed all 3 exploration mission.