First off, let me say this is a great game. I saw the booth at GenCon, picked up the special deal and loved it, and the new beta 2 adds some really cool stuff. The new fire rule is a pain in the butt - very nice. :)
However, there are two thing that have happened with some regularity since I upgraded:
1) Migrants will sometimes appear as Independent units and have to be captured in order to add them to my pop.
2) Slaves will rebel if placed within view of units, but not buildings, so even babysitting them with military units while moving to a location isn't working. And when I mean building, I mean anything but mines; shrines, cities, forts and towers are all good.
Problem 1 is an on again off again thing, problem 2 is consistent. Not sure if anyone else has noticed this, but its kind of frustrating to watch a group of 40 slaves go psycho in front of Phillip and his Hypaspists.