I spotted a few minor issues in my last two games:
>Desert tiles with scrubs on them lose the scrubs if upgraded with Spring, but keep them if upgraded with Vitalize (discovered with patch k as Ljosalfar)
(everything else comes from a Kuriotates game with patch l)
>Genesis upgrades desert tiles under flood plains, and does so without removing the flood plains. The new plains tiles can then be further upgraded with Vitalize, still leaving the flood plains.
>Heroes that abandon you due to a religion change can be rebuilt if you later change back to their religion, or can be be rebuilt by other civilizations.
>Mardero (presumably due to Channeling 3, meaning it would also affect Yvain, Sphener, Chalid, etc.) will not defend a stack until he is the last one remaining, even if his defensive strength is more than 4 times higher than the next available unit. (The Marksman promotion, however, seems to correctly choose the weakest unit regardless of chance to defend).
>Enraged units can be controlled by giving them move orders for the next turn after they have moved.
>Basium's spawn kicks all units out of the city, even though it's still your city until the end of the turn and you have an alliance with him.
>Kraken, due to being Beast units, can gain a variety of promotions that are useless to them (like Woodsman). This probably also means that they can get Blitz.
More Balance-ish issues:
>Herne, unlike all other centaurs, does not receive defensive bonuses.
>Due to jewelers and pearls, the Kuriotates receive a moderate potential boost in all games featuring the Lanun, and are heavily weighted towards befriending them.
>Once casting Hide, there is no way other than finding something to attack to remove the hidden promotion (making it hard to use such units for defense).
>The ability to upgrade priests into Druids (which can then cast higher level divine spells) makes neutral civs far better at channeling divine power than good or evil civs.