Here are some bugs that I have encountered in the last game I played:
Caravans! You kind of got rid of them, but they are still running up and down the roads. While this can be useful in revealing the territory of those you trade with, caravan units drive me nuts! Pathing should not regard them as occupying the space they do. I have all sort of issues with units having to move off the roads to go around a caravan. And even though they are moving on the road, they only move 2 squares, so if you are stuck behind a caravan in a forest or swamp, it's like being stuck behind a semi on a mountain road. They are slow and you can't pass them. They also still say that they are X trips to upgrade the road, but roads upgrade via techs now. Please make them non-blocking units, even non-selectable, or just gone. Also, roads on barren terrain or through forest are very difficult to see.
When you clear a lair in a forest, the tile remains a forest tile, but there are no trees in it. If you save the game and restart, it correctly draws trees there again.
In my last game, the city spells that affect trained troops stopped working. I dispelled them and recast, reloaded from a save, but they still didn't affect the unit stats. I can send a save if it will help.
Something I noticed about the graphics is that if you turn anti-aliasing on, it anti-aliases the city banners, making the text, numbers and spell icons very blurry. It shouldn't anti-alias those, just the graphics.
Another graphic glitch I noticed with my mages. When they shoot over a pond on the tactical map, the shots disappear when over the water, almost like the water is in front of the shot graphics.
I got the alliances tech and created an alliance with Altar, and the next turn a message popped up saying that my alliance had expired. It still showed my disposition with them as allies, and the treaty was still in effect. A while later, Relias popped in to chat, and said "Hey, we should form an alliance!" Ummmmm, we did, genius.
I got the ancient ruins quest that spawns Scrap Golems everywhere. A bunch of them spawned in the water or coast or in a chasm. In fighting them, I cast Titan's Breath and they technically fell over, but there was no animation or prone graphics for them.