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These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Good Bad Bugs: A bug in the original release allowed the player to destroy enemy buildings with the Demolish command, which was only supposed to work on the player's buildings. It was fixed in the expansion.
Don't forget the unlimited Yin cheat.
It Was His Sled: Poor Otomo. Due to plot reasons, he does not survive through any of the Dragon or Serpent campaigns.
To wit, they are the Diseased One, who has knowingly infected himself with plague and coughs it onto enemies with the help of a respirator, the Unclean One, whose body produces toxic mucus that he flings with a lacrosse stick, and the Infested One, who attacks by throwing fistfuls of maggots that he pulls from his bloated, rotting body.
The Geisha certainly counts. In the early 1600s, geisha were mostly known in japanese culture as prostitutes. This, combined with the Art of the "Massage" technique you can research, suggests that the geisha are having sex with your soldiers mid-battle. That isn't the squick part. The squick part is that you can heal wolves and horses this way, too.
That One Level: Serpentholm. You have to fight both the Lotus and Wolf clans, and finding a suitable location for a base is not easy.
To be fair, it's quite easy to set up a base at the central rice field and peasants gathering water from the river can be easily defended. Plus, The Lotus and Wolf clans are also against each other.
The second Serpentholm stage is even more notable for being frustratingly Nintendo Hard. For starters, your starting place in inconveniently placed between flanks of 2 enemy bases on both sides, and the water source is far from your base. As you fend off the oncoming enemies, chances are you are still recovering your troops when the other clan's allied troops come charging in to raze your camp.