I haven't been following the bugs listed by others, but here are the strange things that I've noticed:

Enemy troll warriors and shamans occasionally survive combat, similar to heroes (I suppose this might not be a bug, but perhaps a mention on the Troll's tool-tip or encyclopedia entry would be helpful?)

Missiles will occasionally come from off screen, as opposed to their origin.

Booted out of the game ('Elemental has stopped responding)

Most powerful nation abdicates, citing lack of power

The forge necessary for the spell of making indicates lack of influence as reason it cannot be built, as opposed to seemingly requiring all three towers to be constructed first

An old faction I created in EWoM is in FP, but it functions strangely due to the vast differences in editions (certain research items that permit questing don't seem to show)

Magic damage is inconsistent - when casting  a spell that isn't resisted, on a creature that has no visible resistance, spell damage is occasionally reduced by 30%ish

Shadow Warg model occasionally has a black line stretching out from it.

Tech trades don't seem to show any tangible benefit (although I simply could be missing something otherwise obvious).

My chosen research field appeared to change twice without my knowledge or permission.  Not that I ended up using siege engines, but it would have been nice to have finished researching them when I originally intended.

After a city is destroyed, no new cities can be built on the same land (grain and what-not do not repopulate).