Yukio: How'd you know there was a pool down there?
Logan: I didn't.
It's brief, but during the fight at the funeral, at one point Narada is covering Logan as he leaps into a room to take out the guys trying to get away with Mariko. Narada draws his bow and looks ready to fire a shot to help Logan...but after about ten seconds, Logan's carved up most of the guys and is already working on the rest, and Narada eases up on the bow without firing, the expression on his face clearly along the lines of, "Oh. Well, nevermind."
After the Traintop Battle, Mariko and Logan end up in a love hotel. The only vacant rooms are "The Dungeon", "Nurse's Office" and "Mission to Mars." They awkwardly pick the last one.
When Logan passes out from his injuries, the front desk lady brought her veterinary student grandson to patch him up. It's a Wolverine, after all! When Logan offers to shake the young vet's hand, the latter backs away in terror because Wolverine apparently unsheathed his claws and hurt him while unconscious mid-surgery.
Logan's entire bath-and-shave hygiene session in the Yashida residence. He later quips, "I've been violated."
There's some Bilingual Bonus as well that makes it even more hilarious. One of the ladies says: "It feels good, right?" ("Kimochii deshou?").
Hugh Jackman's remarkable performace making it look a lot like trying to bathe a cat in general.
Logan sticks the chopsticks upright into his food. After Mariko gently corrects him, he did it again!
While on the bullet train, Logan tricks a yakuza to jump to avoid being struck by a low-hanging sign, only for the unlucky bastard to get struck by a higher up sign.
Logan enjoying the reclining train seat.
Also in the traintop battle, the brief cut to Mariko in her headphones while a Yakuza roars at the glass in impotent rage.
When the guards freak out over Logan setting off their metal detectors, he tells them with a completely straight face, "I had a hip replacement."