In my current game none of the 3 buildings that are supposed to grant or level up spy skills or cause a spy to approach the empire have actually done so. The situation is that all my leaders have all their secondary skills filled so none can learn a new one and there are no spy leaders available. However, I do have leaders with spy skills at basic and advanced levels and none of those leveled up--just nothing happened at all. The text does say "up to 2 leaders..."--does that mean it's random by design whether any level up? If not this seems to be a bug. I've attached the game where the Galactic Surveillance Network will be built upon hitting next turn. There are 2 colony leaders with 1 spy skill at basic and one colony leader with 2 skills at advanced--all the ship leaders are already maxed out.
Yes, there was a bug in how the spy leaders gained skills from buildings/events where if no leader could learn new skills, even spy leaders with non-expert skills could not improve their spy skills. The good news is that this only happened if no leader could gain a skill, which was the case in the save you provided. In any case, this was resolved and a fix will be available in the next update. Thanks for the report and the save.