Stupidity: When Castle and Beckett discuss the trap LokSat set for them at the dead drop and any forthcoming retribution, Beckett comments that her dad should be relatively safe from reprisal because he's on business out of town. Someone as smart as Beckett would never make such brain-deadly dumb assumption; considering how powerful and how dangerous he's supposed to be, especially with the resources of the CIA at his disposal, LokSat surely would have no trouble finding and getting to, and certainly no qualms about eliminating, Beckett's dad if it stopped her in her pursuit of him.
Stupidity: When Sonia cuts off her monitoring anklet in her attempt to escape, Ryan and Esposito try to hide the fact from Beckett, an idea that, for the two of them, is absurdly stupid. With at least a decade of experience each, they're too smart to not know that (A) most, if not all, monitoring anklets are tamper-proof (if they weren't, what deterrent would stop criminals from doing exactly what Sonia does and escaping?), and (B) as captain of the precinct who requested her furlough, responsibility for Sonia ultimately falls on Beckett and she would have been notified by the security company the moment they knew that the anklet had been tampered with.
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.