When Magnus say "It nearly cost my friend Jem his life" about the yin fen, it's a nod to James "Jem" Carstairs from Cassandra Clare's other Shadowhunter series The Infernal Devices which takes place in London in the 1870's.
When Alec and Magnus portal into Magnus's loft, discussing sushi and why they call it "fatty tuna", was a conversation improvised by Matthew Daddario and Harry Shum Jr.
In the books, Luke's sisters name is Amatis.
Magnus mentions seeing what Yin Fein can do up close and person to his friend Jem. This is a reference to the prequel series, The Infernal Devices
Maia telling Jace she'd spit in one of the shots she just served him, and Jace's response was ad-libbed by the actors, Alisha and Dominic.