Corrected entry: In the episode 'Trust Me', Syd goes to see her mother at the F.B.I. holding area. Vaughn tells Syd to memorize a series of 3 digit codes to enter into the phone if it rings. In the next episode, 'Cipher', Sidney enters 4 digits. You can hear the beeps as she enters them.
The Telling - S2-E22
Corrected entry: In the episode "The Telling" Syd wakes up in Hong Kong. When we first see her she is wearing a turtleneck sweater. When she is in the safehouse with Vaughn, the sweater no longer has a turtleneck, it is more scoop-necked. She did not have any clothes to change into, nor was she given any.
Correction: She probably was given the opportunity to shower and change by her handler. Just because we didn't see doesn't mean it didn't happen.
Correction: There are 4 beeps because Sydney needs to enter the code, (3 digits) then hit "ok" or "enter".