Flowers for Your Grave - S1-E1
Other mistake: Beckett and Co are in the mental patient's apartment. She opens one of Castle's novels. The title page says that it's called "A Skull at Springtime." However, on the opposite page, it says that the book is "Storm Fall." (00:19:50)
Nanny McDead - S1-E2
Other mistake: When Castle is reviewing the footage of the nanny in the elevator, he observes there is a five second time difference between the two time codes. But there's actually a difference of seven seconds. (00:25:15)
Flowers for Your Grave - S1-E1
Other mistake: Castle's book "Storm Fall" is a bit of an enigma, since it is amongst all the other books in the collection of the scapegoat killer when Kate opens it, but Castle gifts "an advance copy" to her later, while in the very first scene of the show there is a party with the book already in the hands of the public. Reviews and a proper release appear only in the fourth episode.
Answer: The networks are now having winter breaks. A mid season end of new episodes, when they come back after the new year, it picks up as if several months have gone by. Beckett suggested Valentine's Day as a "chick flick" to watch as she is moved in. Also some episodes are not scheduled to air in order.