syntax-quote can cause this:

  > (type `(1))
  clojure.lang.PersistentList
  > (type `(1 2))
  clojure.lang.Cons
  > (list? `(1 2))
  false

edit: however http://clojure.org/reader#syntax-quote does specify that syntax-quote is not the same as quote for some forms, including lists.