Add this one to things lost between saves in 1.65. When I loaded a save I lost all the loyalty bonuses I gave my leaders by providing harmony crystals, coupled with the leaders having very low loyalty stats in general, the have base of 34 for some reason, this is a big annoyance.
Not the only thing lost, Many of the anomaly and cultural upgrades and artifacts disappear on reload. Speed, scan and other buffs. I mostly see it with ships it is like the game does not save the upgrades on save so you return to base ship. Upgrades like command bridge from experience stay but any buff from events or the culture tree even scan buffs from the tech tree disappear on reload.