1. In a city connected to 2 Clay Quarries, the total materials is correct, but the tooltip only shows +2 materials for 1 Clay Quarry.
2. Not sure if Tremor is removing dodge properly.  Shields grant dodge, and that stays after a Tremor, but I think sometimes the native dodge is not removed correctly.
3. There is no way to tell what size a unit building in the build queue is.  Build queue tooltips in general need more information.  A finished/total production would be nice.
4. When you cast Shrink on a Juggernaut, it has 0 attack and does nothing all fight.
5. In the Build menu, when you select a building that reduces unrest, it shows the new values for unrest but does not show the resulting change to production and research that the reduction in unrest would give.
6. Buildings do not show in the build queue until you close the build menu.
7. When you have cast the same enchantment on multiple units of the same type, there is no way to dispel the enchantment on a specific unit.  All the units in the enchantments list look the same.  Perhaps add an X button next to the enchantments in the unit details as an alternate method of removing enchantments.
8. Boots of the Spider are not really useful.  They cost 2x that of a horse and only grant one of the many benefits of a horse.
9. Units that are prone can still dodge.  Prone units should have 0 dodge or at least reduced dodge.
10. Also the animation when attacking a prone unit is odd.  The unit stands up, runs over to the attacker, then lays down again, get beaten, then runs back.  No movement animation is necessary.
11. City icons in the left toolbar do not update the production amount progress bar when you rush buy.
12. AI does not seem to be upgrading any of its resources.  I assume this is in the works.
13. When editing an existing unit design, some traits or special equipment can become stuck, so that you cannot remove them.

Also some suggestions:

1. The info area above the minimap that shows the terrain type and movement multiplier should also show the owner of the territory.  It would be nice if it also showed the number of turns for the selected unit to move to that location.
2. The cloth map should show a similar icon on the town center as the 3D map does to distinguish Towns, Fortresses, Conclaves and villages.

Also odd, I saw Pariden's capitol around turn 250 and it had 2 materials at +6 production per material = 12 production!   All my cities are 30-80.  I think it was a Conclave, but why is it completely ignoring production?