Why is Yuki surprised by the Level E vampires?
It's apart of Yuuki's denial that Vampires can be bad, don't forget her earliest memory if that of her idolized Kaname soaked in blood yet she doesn't fear him (at first). Also as a Guardian all the other Vampires she has met are in the Night Class and none of them are like the Level E she encounters.

We see later during the the first part of the series Yuuki trying to deny that the Vampires of the Night Class, particularly Kaname, and the Level E's are the same blood thirsty creatures but Kaname tries to make Yuuki understand they are the same by letting her see him drink Ruka's blood being fully aware Yuuki was peaking though the door. he did this knowing


   that if Yuuki is afraid of Vampires she wont want to return to being one


i also suspect that when Yuuki went into the Night Class Dorm during the day and almost had her blood taken by Aidou Kaname was well aware the moment Yuuki entered but also knew Aidou was awake. making sure to stop Aidou at the right moment