I'm currently in the process of updating this list to 1.3b.  Anything with [] before the number has not been checked yet in 1.3b.  I removed issues I confirmed to be fixed.  

Here's a bunch of minor bugs that I didn't feel were worth each getting their own thread.  I'll probably add more minor bugs to this thread.  Feel free to contribute.  I can add to the list here so it's more noticeable.  Any missing numbers are issues that have been confirmed fixed.  Minor bugs only!

4. IconforGrowth in the Empire Tree doesn't match the icon in the build menu and queue.

5. Number of turns for construction shown in the city HUD does not update when city production changes due to unrest.

6. Edge scrolling left and right is fine, but up and down is very slow.

8. The Ogre Camp improvement doesn't show up on the Cloth map (the tile just appears blank).  

9. Event List still overlaps the minimap.

12. When you run out of mana, it cancels all of your enchantments.  Not just the ones that have a mana maintenance, but all of the city enchantments, too.  It shouldn't cancel those.  It should only cancel enchantments with a mana maintenance.

13. If the name of the improvement is too long (Tower of Dominion), it doesn't show turns remaining in the city HUD.

14. Quest where you can trade 3 wolf pelts for a cloak: You should be able to trade the wolf pelts when getting the quest if you already have them. Currently you have to leave the square and then move back onto it to trade him the pelts.

[]16. Storm Dragon faces in random directions when using the breath attack.

23. Armor and Heavy Armor tech tree descriptions do not change to accomodate the Light Plate and Masterwork Chainmail faction strengths. -N1ghthavvk

[]27. Auto-resolve doesn't work right for abilities that hit more than one tile (AOE attacks); e.g. Impale, Cleave, etc. all hit every unit in the opposing army (and the damage looks weird too; I think it may not be applying armor correctly for the "extra" units that get hit, but applying it correctly for the couple of units that are actually supposed to be hit by the ability). - ArisianOne
[I don't know how to check this one. -Darxim] 

[]28. Auto-resolve doesn't work right for Air Elementals; their Gust of Wind ability does large amounts of damage to every unit in the opposing army (Gust of Wind makes units Prone, but the actual version cast in tactical combat doesn't cause any damage). - ArisianOne
[...or this one. -Darxim]

[]29. Caravans can "shield" units. If a hostile army is in the same tile as a non-hostile caravan, attempting to attack the hostile army instead takes you to the diplomacy screen for the caravan's owner.  This means the enemy army is essentially untouchable until they move to a tile that doesn't have a caravan. - ArisianOne

[]30. [maybe at least partially fixed] Spider AI (particularly Black Widows).
[I haven't been running ranged units in my current game, so I haven't been able to see if Beguile's truly been fixed as claimed, and if Web has been fixed. -Darxim]

[]31. Units with the enchantment Nature's Cloak sometimes leave a copy of their (green, sparkly) particle effect on the world map when they leave a square. After a while of running around an area, you are left with green sparkles everywhere. Goes away if you quit and load from a savegame. Possibly appears after combat? -ArisianOne
[I never saw this occur since I almost never used Nature's Cloak.  I've been using it in my current game on every champion, and I haven't seen this occur yet, but I'm not assuming it's fixed since it says "sometimes". -Darxim] 

32. Only one of Life/Death magic trees shows up in the "Traits" window (whichever is appropriate for the sovereign). This is a problem when dealing with surrendered heroes from the other alignment; there's no way to add points to the skill when leveling up, because the skill doesn't show up. Also, it's possible to use "steal soul" to give a single sovereign both Life and Death magic, but again one of them will be impossible to see or level up. -ArisianOne

33. The Plague event quest does not tell what the (extremely high) mana cost of the Cure Plague spell is when choosing a solution. -ArisianOne
Solution: Add the bolded text below to CoreQuests.xml:
<Description>Cure the Disease (-50% Growth until you cast the Cure Plague spell)</Description>Change to: <Description>Cure the Disease (-50% Growth until you cast the Cure Plague spell which costs 500 mana)</Description> 

34. Blacksmithing military tech text mentions creating Maces, but these are now unlocked later in Weaponsmithing. -NaytchSG

35. Cooperation text talks of Pubs and Missionary Halls, but does not unlock them. -NaytchSG

37. A city's Zone of Control is not visually updated the turn that a new improvement finishes construction.  The new ZoC actually does apply practically, it's just not displayed.  The ZoC display can be force-updated by building an improvement on a resource, and will remain updated even if that improvement is canceled (this information may be helpful in fixing the issue).  -jonasadolphson

38. Cancelling a Troll Lair's construction does not refund the 100 gildar.

39. City Curse icon does not disappear until the turn after it is dispelled (although the effect does end immediately).

40. When selecting Black Market in the Build menu, it shows a reduction to Research and Production, presumably from the Unrest increase, although it does this even if it wouldn't increase the Unrest above 0.

41. The load screen text for shards shouldn't say "damage multiplier for some spells", but rather "improvement to some spells" or something like that, since it often improves things other than damage, and the damage increases are static amounts, not multipliers.

42. When casting Raise Land to make a path through the ocean, the land often doesn't break through the surface of the water, so you can't tell that there's a path there without going into the cloth map and seeing the squares (and that's only if you have the grid turned on).

43. After clearing a Lair that's on a Forest tile, the Lair graphics clear, but no Forest graphics appear to take their place, giving them the appearance of a Plains tile.

44. When an AI player (not sure if it's also for the human player) begins casting the Spell of Making, and their sovereign is defeated in combat before they finish, the progress bar for casting Spell of Making continues.  The spell doesn't resolve at the end (hence this being a minor bug), but the progress bar continuing makes it look like it's going to complete no matter what you do other than wiping out the entire faction.

45. Ranged AI units that have been webbed will not attack.  They simply pass instead of attack while they are webbed.  My ranged units can still attack when webbed, just AI units won't.

46. Tangled Web's description does not mention that it reduces dodge to 0.  It makes sense that a unit couldn't dodge while webbed, but the description still needs to state it.