If you run the Jouret System patrol mission there is a bug based on which the order of the satellites you repair that will prevent the enemy ships from entering the system. If you repair the com array, then the satellite nearest the planet, then the other satellite the ships will not appear. If you repair the satellites in any other order they will work fine.
I've run into this bug several times as well, but I've seen it happen even when repairing the satellite farthest from the planet first. I had it fail twice in a row with one character, then took a different character in and succeeded 7 times in a row without failing at all.