At the end, Castle asks Lucy to turn the lights down and they do. After this, a male voice asks if the lighting is OK, and it is revealed that Beckett changed Lucy to Linus. The lights shouldn't have turned down because Castle didn't say Linus.
When Sonia cuts off her monitoring anklet in her attempt to escape, Ryan and Esposito try to hide the fact from Beckett. But since most monitoring anklets are tamper-proof, as captain of the precinct who requested her furlough, Beckett is ultimately responsible for Sonia and would have been notified by the security company the moment Sonia cut the anklet off.
It seems out of character for Esposito, a 10 year plus cop and Special Forces vet, to not call in back up when confronted with an open door apartment, particularly when Ryan is downstairs and Esposito has a civilian with him.
It seems a bit out of character for Ryan and Esposito to blindly accept how quickly Castle and Beckett reconciled without, at the very least, questioning what happened to "Svetlana", since in Tone Death (2016), they were both so convinced Castle was cheating on Beckett that Esposito had to intimidate him into "admitting" it.