1) Got a notice about the Solar Eclipse, and it said that all player monster characters get +2 lvls. I had three cave bears in my leader's party, and they did not get a bonus. ... Or does that only apply to the fallen races and their allies?
2) Some of the researches disconnected and their names and research times vanished from the research trees. All the second and third from final tiers in the Civilization tree, all of the first and second tiers in the Military tree, and a couple random ones from the Magic tree. It fixed itself after I completely quit the game, only to happen again a number of turns later. Not sure how long.
3) Not sure if this is a bug, but in the Varkana quest, the one with the dog that went feral with the wolves, if you tame him and return to the inn, you can only lie about killing him, or tell him that he went feral and got put down. Nowhere was there an option to return him back to the hunter.
4) When building in a city, turns required when in the build menu and when on the build cue will sometimes differ. Suspect it is liked to the town bonus that gives +1 production per material, in that the build menu shows it correctly, but it isn't factored in when set to actually build.
5) AI controlled cities have the possibility of spawning a frankly ridiculous number of defenders, some of which don't even spawn in the city. Fought against the Magmar fortress, path lvl 3 capital, and they had 10 assassin demons, 6 militia, 14 guardian idols, 5 fodder, and 3 archers to defend the city. Unusually large numbers appear to be tied to the guardian idol city upgrade.
Will update later as more are found. Feel free to add your own ones here.