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The coolest bug is the city specializations... They promised to fix it in Tribes of the East, but it's still messed up... (At least in the online version, it doesn't work, and I have a licensed copy). Also, when playing as Dwarves, my troops would get stuck in the tower and couldn't move (or is that how it's supposed to be?). And then there's the orange city – you can read about it in the humor section.