At one point in the manga, Kaname tells Zero: "I envy you, you who can protect the girl you love". People at that point naturally assumed he meant how Zero was able to directly protect Yuuki while he wasn't. Then in chapter 61 and beyond we're introduced to Kaname's past where he knew a mysterious pureblood woman who ended up sacrificing herself for the creation of hunters. Kaname reveals how he was the one supposed to have sacrificed himself instead and is shown mourning her memory in some occasions, implying she was the woman he thought of when telling Zero what he did, not Yuuki.
Kaname somehow feels a need to lock Yuuki in their home in the second arc to keep her from danger, even though purebloods can't die, or are very difficult to kill.
A vampire hunter is ambushed by a pureblood at a ball early in the second arc, even though vampire hunters are supposed to be able to detect vampires from long distances. Similarily, neither Yuuki or Zero seem to know Aido is spying on them at one point. Purebloods can also sense each other, however Kaname still seem unaware that Yuuki is just standing a few feet away from him while she's evasdropping on a conversation between him and Kaien.
There's apparently a huge amount of level E vampires as implied in the second arc, however only a few purebloods exist, and none of them are said to turn humans for fun, leaving the question as to where all those level E's come from.
At the end, it's revealed that Kaname had been working on a cure that transforms vampires into humans. In that case, why didn't he continue with that instead of going on a genocide mission that ended up in a Motive Decay?
How does Yuuki know the human spell won't eventually break for Kaname, who was possibly the most powerful pureblood and vampire in general, when it broke for a weak pureblood like her?