Either an author's mistake or a very sly bit of foreshadowing.
by Cassandra
1. if Harry's mom was a witch, then why on pg. 646 does You-Know-Who say "A Muggle and a fool....very like your dear mother." was she a witch, and if so, why does He call her a Muggle?
You'll have noticed that in The Chamber of Secrets, Tom Riddle also calls Harry a halfblood - it's these two instances that make me think that Voldemort is obviously missing some vital fact about Harry's heritage, one which is likely to do him harm.
2. if Tom Riddle and You-Know-Who are the same person, how is he alive today? I thought he was killed a long time ago when he was a child? AND if he was killed by Him, how is that possible- they are the SAME person?!
... I don't know where you got the information that said he was killed. His mother did die giving birth to him, but Tom Riddle AKA Lord Voldemort is indeed alive and very well . . . at least, he is now.