I will continue to update this post as I find more and more bugs, and will do my best to remember to take screenshots when relevant and possible.  With that being said, I may revisit certain bugs/issues as I progress along.

[Bug] Fog of War rendering failure allows me to see gigantic beams of light or erupting explosions at all quest/resource locations.

• I couldn't think of a better description for this one.  Despite many resources being hidden (which I later explored to verify), I was able to see these strange graphics.  There appeared to be a different graphical mistake for each 'important location' archetype:  Giant beam on buildable resources, explosions on monster lairs.
• This bug occurred upon loading an autosave after playing the game for approximately 20 seasons.  Reloading the same autosave removed the graphical issues.
• Will include screenshots if it occurs again!

[Bug] Killing the beast army guarding a Monster Lair removed the Lair.

• A rather frustrating bug.  My first few monster lairs (a well guarded by a butcher and a Black Widow guarding its domain) allowed me to loot the space after defeating their guardian.  The next three (a bear lair, wolf lair, and fire shrill lair) immediately disappeared from my map after defeating their respective guardians.
• After defeating the guardian, moving to the space where the lair was originally placed (before it had disappeared) didn't allow looting, either.
• Luring the guardian away and sneaking the loot away proved effective, albeit a bit underhanded.

[Bug] Autosave 'saved' my army from being attacked.

• Originally, my army moved too close to a monster army that decided to end our miserable existence.  Intending to be more careful next time, I loaded up my most recent autosave; it happened to be the beginning of the turn where my army was destroyed, but this time the monster army stayed put.  After reloading this save several times to be sure, it seemed as if the monster army's turn was skipped.
• Very exploitable. Reminds me of the original, E:WoM.

[Issue] Tactical tile spaces

• I sometimes had trouble clicking the precise square I wanted my unit to move to, especially when large/numerous opposing and allied units were near said spaces.
• Couldn't tell the difference between 'blocked' terrain tiles (such as boulders); I eventually learned the difference through trial and error, but having some in-game differentiation would've been less painful.

[Bug] Case of the Missing Healthbar

• This enemy group attacked mine from a Monster Lair.

[Bug] AoE spell can't target ally, must hit enemy.

• Normally, this sort of set-up can make sense; but I physically (given the positioning of the enemy and my troops) could not hit JUST an enemy. I wasn't able to dispel or cancel the spell, either! I would've gladly accepted a voided turn, but I had to use Autoplay to get through the battle.
• Need some form of channeled-spell cancellation!

[Bug] Too much mana...?

• Unless I'm missing something, I appear to be getting 48 mana per season when I should be generating 3.
• [Update] My civilization had 3000+ mana within about 20 seasons, so this rate seems to have increased dramatically!

[Bug] Where'd the water and buildings go?

• Seems to be a memory leak issue; upon reloading a save file after playing for a while, I received this little rendering tidbit
• The image shows it all.

[Bug] Hidden Monument?

• After throwing several legions of soldiers to soften up a dragon, I finally conquered it and obtained building rights to a special fire-shard tile.  The tile itself looked amazing, so my hopes for the monument built upon it were high.  Upon queuing the spot for building, the visual promptly disappeared from my map.  Reloading didn't solve this bug, either.
• When I queued it to be built in my main city, the site showed 'three turns', but my town still said 'no construction'.
• The monument is actually there and provides its benefits, but no visual outside of the cloth-map mode!

[Issue] Notifications are given at beginning of turn BEFORE opponent-initiated combat.

• This was one of the major issues I had with E:WoM.  I would receive a notification that my research completed and that an opposing nation contacted me, click to respond, and be immediately bombarded by a 'combat notification' overlaying ALL of these.  In other words, I was forced to go through the combat before making these diplomatic/research decisions, meaning that I had to keep track of all notifications and act upon them after combat was done.
• Simple-sounding solution, depending on the game's engine:  Give combat notifications first, then after ALL combat is done, display diplomatic, then research.  Perhaps other notifications would be higher/lower than these listed, but it's a general idea for hierarchy.

[Bug?/Issue] Torax was hit about 9 times by a single fireball.

• I assume the fireball hit every square he was in, resulting in such a massive single attack.  This seems like a bug, but I also take serious issue with the 'nuke from orbit' concept when the nuke costs a mere 10ish mana (after my many mana-reduction items/skills).
• I've had other issues with the Fireball spell noted previously, and I'm sure I'll continue to find more.  Definitely a spell that needs some looking into!