Revealing mistake: Dean borrows Charlie's phone to call Sam. On the phone, the lock screen can be seen, showing that he never entered in any number.
Continuity mistake: During the scene when Sam and Dean enter the abandoned shipping warehouse to save Charlie, you can see Charlie's legs crossed while sitting in one shot, but in the next shot they are uncrossed. (00:27:10)
Answer: Angels themselves may not have genitalia, but their vessels do. Nephilim occur when an angel in a vessel reproduces.
Greg Dwyer