The game is bugged. Having said that, many bugs are easy enough to avoid. I'd like to post some of my observations (most of them are carryovers from the original FE).
1. If you're going to reload from a save, quit the game and load from a freshly started instance. Minimizes crashes almost to the point of non-existence.
2. If you're saving the game, make sure that none of your units are scheduled to move further than their movement points allow. Otherise upon reload they'll end up at their final destination instead of where they should have been at the end of the turn. Yes, this can be exploited.
3. Don't trust the pathfinding algorithm: move your armies 1 square at a time.
4. Don't kill Wildland bosses outside the borders of their respective Wildlands, otherwise the game will have trouble recognizing that the the Wildland has been cleared. This usually happens when the boss is the last denizen of the Wildland(which is quite often).
5. Don't attack the Deocryssus(sp?) city in the Shroud Wildland if its garrison has wandered off: taking the city without a battle does not properly clear the Wildland.
This is what I can think of at the moment, but there's more, lots more. Please feel free to add.