At 52 minutes in Christina sees the black door that wasn't visible moments before Emmett tells her the "closed system" is everywhere. The hidden door is a rewrite from S1 when Bernard doesn't see the hidden door at the off site lab in the frontier house.
The zhuangzi is an ancient Chinese philosophical text from the late Warring States period.
The first piece played on the keyboard during the dancing scene is "Sarabande" by George Frideric Handel. The first four notes are the same as those of the mind control mechanism's sound.
At 18 min in, the 2nd song of organ music being played in the street scene is "Perfect Day" by Lou Reed.
At 18 minutes in during the street dance scene, lettering on the smaller of the 2 man hole covers spells Manhattan.