Simply put: Stains are only gained by acts listed in book such as creating a ghoul, events causing harm to touchstones, bestial failures, and breaking a chronicle tenant.
why else would you, as a storyteller give a character a stain?

The part that says "The more usual corruptions and deformations of the character’s humanity can cause Stains on their Humanity track." does that mean that the character that kills with a humanity seven should gain a stain no matter what? If they plan to destroy an anarch that is causing them ill, is that murder since they are undead?...