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.
Renoir returning to Raphael's lair and asking to be taken back as his student, kneeling down to him... and then Raphael kneels down as well and responds with "Welcome back, my student". Made this troper smile.
Leonardo's friendship with the ninja Sadao. Flashbacks show how rocky (to say the least) their first encounters were. To see how far they have progressed since then, to the point they are implied to often work side-by-side now, is a ray of hope in an otherwise very dark story.
Nausea Fuel: Frequently. Characters vomit on panel, mangled corpses abound and there's plenty of blood from the second panel on.