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.
Foe Yay: Jin really hates Ittosai. So of course the moment he shows any concern about why he's not back from fighting off ninjas, Bo asks if he's worried about him and Yo pipes up with, "Are you saying the more they fight, the closer they are? Are you...slashing them?" Bo then asks if he means slashing tires.
Ho Yay: Toyed with in game on occasion. Muneshige and Mon-Mon have a couple of scenes that even make Sayori uncomfortable. Harumoto and Kasumimaru have a moment or two as well.
Kasumimaru: "Forgive my presumption, but I have no desire to be promoted. I only wish to stay by your side and serve you as your shadow, Lord Harumoto."
MST3K Mantra: If you try and figure out why a bunch of medieval samurai know pop songs, your head will hurt. If you just laugh at the jokes, it will go much more smoothly.
Woolseyism: Most of the translation is very close to the original Japanese, except in cases of things like puns that just aren't funny if you translate them word-for-word. Those get an equally-silly English equivalent.