Ok, so this is my accumulated bug list for this last game, which I actually played *gasp* through to the bitter, bitter end (it took forever)...
FFH2 0.30a, Huge Map, Modified FFH Smartmap, Epic speed, 14 civs., Player as Luchiurp on Noble or Prince (doubt it matters), Using Runes of Kilmorph as my religion all game long (very little incentive to switch, tbh

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Ok, so, not all of these may be bugs. There were a number of "bugs" I "found" which later turned out to be design or interface decisions I hadn't expected. So, if I erroneously report some non-bugs as bugs, my apologies 8).
Bombarding units can move to the end of their movement (all mp spent) and then bombard. This also goes for fireballs.
Boats can use all their mp, bombard and then blockade.
NPC factions commonly request resource trades for resources they already have (which I don't believe occurs in regular civ, nor has any meaning for non-mana resources).
Rune of Wardings are off-center on large cities. I'm not familiar enough with the LSystem for cities, this may not be easily fixable, but, I did notice a lot of off to the side warding circles on many of my larger cities.
Summoned units (Earth Elementals, Balors, etc.) can capture cities. I thought I read somewhere that summoned units were supposed to be incapable of such.
You can not build a lumber mill on an Ancient Forest.
Also, despite chopping down a good number of Ancient Forests (Arendel attacked my poor friend Arcturus you see), no tree ents showed up to explain to me how I aught to know better.
Maelstrom effects boats, as do fireballs and meteor storms. This is probably as intended, but I was still surprised

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Stonewardens can't pillage.
Skeletons (the permanent summoned kind) also can't pillage. Neither can hippogriffs.
Conversely, Earth Elementals, Imps and a few others can pillage. Somewhere, something here seems odd with the pillaging.
Mud Golems built in cities with a Fire Mana workshop (I forget the exact name) can cast fireballs. This may be intended, but it's damn funny looking 8). And mean. Definitely mean.
The Large Elephant Stables, as near as I can tell, do not work, and do nothing. Similarly, captured elephants are nigh useless, and can not be upgraded to war elephants.
Wither doesn't effect workers. Neither does Haste.
As part of my end game dance to avoid more armageddon, I tried starving cities by surrounding them down to size 1 before capturing them. Quixotically, although size 1 cities usually are razed automagically when you capture them, starved size 1 cities can still be captured. If you choose to raze them, however, you incur no AC penalty. Sometimes, it seemed like you even gained AC.
Also, Sanctify seems to be behaving erratically. Although generally Sanctify lowers the AC, it only registers after you end your turn, and the amount of AC lowered is disconnected from the city sanctified. You can sanctify city ruins of sites which cost no AC (because they were size 1) and still gain an AC lowering benefit. You can also sanctify the ruins of large cities and gain no AC reduction. Very strange.
Razing barbarian cities raises the AC.
Seas of Rage seemed overpowered. When it was used on me, the only thing that kept me from losing the game was the lack of any actual attacks coming at the same time. Used with intelligence, Seas of Rage seems like it would be an I win button against any one civ. Conversely, Golden hammer is very nice, but not an I Win button. The Sidar all my units are invisible for one turn seems relatively underpowered in comparison to either. The Worldbreak spell is problematic as no computer player seems to have the slightest idea how to put out fires. Some sort of computer handicap might be necessary until the AI can be improved (increased chance for fires to go out in a computer player's cultural zone, modified by number of water nodes?).
Cardith's city limit seemed quite severe on my map size, where he was limited to five cities. Does the Cardith city limit scale with the size of the map?
Catapults do not upgrade to Canons.
The AC went down after I razed one Tasunke city. The AC counter went down again when I sanctified the site.
Sometimes Haste (I wrote down about Bambur, but I think it's general) when cast on units which are already out of mp will grant the promotion without granting extra mp. Sometimes the mp is granted, but the green/yellow/red movement state icon doesn't update.
When you gain access to Paladins, you can no longer build Soldiers of Kilmorph (even though Paladins are limited to three). This sucks 8).
I found the Dragon outside his city, presumably as the result of attacking someone who walked next to him. It seemed strange to me that he would leave his horde unprotected. When I killed him, I received relatively little xp (maybe 5 or 6?). As opposed to the Lich who gave me 25ish and a staff. Of the two, the Dragon is harder. Also, the staff's "Death Affinity" did not appear to be working for me, at least not until I made that caster into a lich, then it became less clear.
Mithril Golem -- Despite having every tech and every building, I could never build this one. Perhaps it requires the Kilmorph special holy building (I never got a great prophet

), but the civopedia entry makes no mention of such a requirement.
Similarly, I could not build any Dwarven Shadows.
Despite having the ratcatcher's guild and some very high crime rates for large portions of the game, I only encountered 1 crime event.
In the Talented Juggler event, I was able to select the Priest of Leaves option even though I had no Fellowship of the Leaves cities anywhere on the map.
Using haste to gain the mp to upgrade a unit, for example, from adept to conjurer, etc. deprives that unit of its free promotion.
Under the write up for Dwarven Druids, it says you must be Neutral, but they are the special unit for Luchiurp who is Good. Taking on a Neutral religion does not make you neutral anymore (as I think it did in previous versions). Somewhere in here seems like there is a bug.
Golem Fireballs are uneffected by the Tower of Elemental Mastery
Duin the Werewolf hero can not take Commando.
I could not build any Bear Totem buildings, despite having all the requirements listed in the Civpedia.
Many units with split off/def do take "def" damage when hurt, particularly by collateral damage. Sometimes (often?) this is just a display bug for their strength, but sometimes (often?) it isn't.
You can Hurry (with gold, in my case), the Tower of Mastery. That seems wrong. Only cost me 14k gold. Deal at twice the price given the amount of time each turn was taking 8).
If you surround a berserker werewolf, and use fireballs to empty a city, the werewolf will capture the city for the barbarians when it turns rabid (reverts to being Barbarian). This is a nice cheat for getting around razing cities you neither want to keep nor leave in the hands of your enemies.
Some possible bug/suggestions as well:
The +40 Armageddon effect was mad, crazy devastating. I know it's called "Armageddon" and all, but it really knocked my empire on its knees. The Computer players were less effected, owing to the fact that their infrastructures were much less well developed. If it could be graduated a bit, that might work out better. Also, and I tried to test this, but didn't manage it, if you trigger the +40 event, and then use Sanctify to get below 40 AC, do you trigger *again* when you hit +40 once more?
Starvation is a bit out of control. Once a city starts starving, it loses a population level a turn (because the food bank doesn't get refilled after the "logical" subtraction of the food deficit). Given all the ways to suddenly be lacking in the ability to feed your populace, this seemed a bit crazy to me. Perhaps some sort of reverse granary effect would be in order to make starvation (and the effects which cause it) a bit more under control.
Seems like there should be some benefit for capturing the palace of another faction. Given that they all provide mana, perhaps a free mana source of one of their built-in 3. Not a bug really, just a thought I had written down 8).
Are the chances of earth mana generated mineral specials scaled with the size or speed of the map? By the end of my game (about 600 turns) I had cities on my starting continent with 5-6 extra bonus resources. With only 1 earth mana. This seemed a little extreme. You know it's dubious when you start thinking, "Ah man, that's only a copper resource, I got screwed!".
A spell that would create a fresh water source, perhaps as a ritual taking some number of turns, etc. would be very valuable for those large land masses where no fresh water is available.
Also, after using a spell which creates a unit (fireball, summoning, etc.) it would be a nice interface effect to automatically switch the selected unit to the newly created "spell" item (e.g. the fireball).
I thought I had spotted more useful information, but I guess not. Anyway, hopefully these help.