1. The team specific fog of War options isn't aligned to the correct team if the replay was recorded from a player who started in team 2's position. What happens is that, although the fog itself actually does work correctly, the objects the 2 sides can see are reversed. This will result in one team seeing nothing within the "lit up / fog removed areas" but the other team will see what they would normally see within their viewing range, but yet the fog of war covers them, shading out those objects.
2. When the Force Commander upgrades with the Terminator armour, the game removes him from the captain's-slot on the interface and places him with the normal units. At which point, a standard unit for that player then moves into the Captain's-slot.
3. A fallen commander doesn't regain his tool-tip icon (the one that appears above his head during play) and his health bar when he is revived. These are removed when a commander falls, but are not being brought back when revived.
4. Changing the fog of war after a replay has stopped (playback over), doesn't actually change the fog of war itself and only reveals the objects under the fog of war. However, as the fog of war isn't removed, the units that were previously concealed are shaded out.
5. Since the latest updates, you can no longer pause a replay. This means you can no longer take awesome screen shots from within the middle of the battle.