Now that the 'organised' patrols are gone it seems to me that a lot of folks will miss out on what remains.
I rolled a toon on Redshirt yesterday to keep me busy until Holo came back up. Today I find that there is no way to know that you can patrol individual systems for xp. (luckily I read patch notes)
This must have been what I was seeing the last couple of days. I had some Old Patrols left on my mission list that held over for the time I was on F2P Tribble. When I did them I found I was getting rewarded after Each System instead of at the end of the Patrol.
I got 434 Skill Points, and 374 Bridge Officer Skill Points for each system.
Some way to keep track of which systems you've visited would be very helpful.
I was just doing some Freelance Systems at one time, and went into several systems just for the fun of it. When I took the Patrol Missions for those sectors, I could not go back into the systems I had already done earlier. I don't think your worry will be a problem.