I did the same thing after finishing the main quest. I saw the objective "Locate Watchtower Array Hub Kappa" down in the "Activities" section. So I located and destroyed it and then the remaining three ending with Omega. What I didn't realize at the time was destroying the major arrays also eliminates the minor associated arrays. Also, once you destroy Omega, Harper will no longer accept any intel and she'll tell you that you've destroyed all the listening posts. Not really true. You can still locate the listening posts, but the computer will say something to the effect that the array location has been purged. That is true. At that point, you can't spawn the minor array. I ended up going back to a save that I made right after finishing the main quest, The Last Watch. At that point, I had only destroyed Alpha. Then I progressed forward and carefully went after each minor array associated with whatever Major hub was showing in that "Locate Watchtower Array Hub XXXXX" objective. If you want to spawn as many possible encounters with Watchtower ships as possible, you're probably going to have to back track until you have some major arrays left. Even if you go back to where you destroy Upsilon and have Omega on your activity list, that will give you 29 minor arrays connected with Omega. Both Upsilon and Omega have are 30 array hubs, 29 minor plus the major hub. The other hubs, Alpha, Kappa and Omicron have smaller hubs.