Bugs I've found so far:

1. The whole friendly fire thing, that is missile units killing themselves when they are overlapping each other (never put your hastati on fire at will mode in the middle of a big melee, ouch)

2. I can't order groups of guys to run. If I want to charge some grouped hastati through a gate for example, I have to ungroup them first, otherwise they'll just walk through.

3. Sometimes units just sort of forget their orders. I told some Principes on the flank of a bunch of barbarians to charge, only to have them walk up to them and just stop within a few feet.

4. Sieges against towns with wooden walls suck. You can park your archers/onagers close to the city walls and have a field day firing at the guys inside because they just run around in circles (literally). Also, while not a bug, it kind of sucks that there are only a few locations where you can breach the walls, and even then the size of the holes are always really small. It would be nice if I could knock down big sections of the walls so I could squeeze more troops through.

5. Enemies camping in the plaza during a siege can just be picked off with missile troops, they never go out to fight.

6. The battle advisor keeps telling me that the enemy is deploying on top of a hill even when they're standing in the middle of an open plain.

There's probably more, I just can't think of them.