OK, you can get spy points at least 2 ways that I know of: use espionage teams, or "rescue" enemy life pods.
So, I have espionage teams on the enemy's home planet. They've been there a while... then, when I "rescue" some pods, I gain knowledge of a system* (see below for the possible bug here). The espionage team gets bupkis - no increase in their skill, even though they seem to have done the lion's share of the work.
Shortly after that, I recover a LOT of enemy life pods, and a few turns later, the espionage team gains gravitational survey knowledge of a system and gets their skill increased.
So, it seems it all just gets pooled, and the espionage team only gets their skill increased if they are the ones who happen to put the total over 100? That seems... poorly done.
* possible bug: the system I gained knowledge of shared a name with one I already knew... but it was a different system. Also, the Galatic map errored when I tried to look at it, then loaded, but attached that new system somewhere it obviously wasn't... conveniently, when I got grav survey from espionage later, it was of the system that dopple-ganger system properly attached to, and the problem went away. Should I mention this in the bugs forum, or is it too small/already known?