Listing a few of the better known simple coding errors in the current game:
1. Tunisian port graphic is in the Sea of Gabes, but the actual port/merchant/troop embarkation point is the African Coast. Historic info I've seen suggests the port should be in the Sea of Gabes as illustrated, but that the order of the sea zones was accidentally reversed leading to the current mismatch.
2. Mounted crossbowmen should not be available until the invention of the crossbow like the other crossbowmen and arbalests ("High" period rather than "early".)
3. Various minor factions lack "offices" for governmental buildings (chancellor and the like) except for Swiss and Burgundians. Handicaps the other minor factions since they lose command stars and/or acumen for various leaders.
4. Footknights are not buildable (without mods of course.)
5. Rains incessantly.
6. Autocalc doesn't properly handle castle sieges, fails to calculate significant losses for attacker due to fortifications--particularly when the attacker lacks siege equipment.

Couple of things that might not be true "bugs" but certainly don't fit with the rest of the game...

7. Varangian guards are not available to the Byzantines in Late. The Byz are already handicapped by the lack of spear units in Late. Taking away the Varangians is a pretty heavy blow to add to it.
8. Polish Retainers should be available in more than a single province (a few neighboring provinces would make sense.) They are of little use to the Poles because of this restriction.
9. Lithuanian cavalry is at least one full set of building upgrades above what it should be when compared to other cav units. Why the "Swordsmith3" requirement for lance armed cav/archers? Shouldn't this be "Spearmaker2" or "3" or something? Why "HorseFarmer4" for *light* cav?
10. Dismount choices for many cav/camel are a bit strange and the Muslim units really have poor selection--seems like they should get some sort of "special" upgraded version of the equivalent foot unit that they presently have. Afterall, the men in question would likely be better fed, better armed/armoured, and of higher morale than their counterparts.