The mugger who tries to mug Barry and Ralph is the same mugger who tried to mug Barry in season 1.
When Harry was talking to his doppelgängers, a doppelgänger of him interrupted and said, "I am Wells the Grey", an obvious reference to Gandalf from the Lord of the Rings.
Cisco refers the group of Wells as Council of Wells which is most likely a reference to "The Council of Reeds" from Marvel Comics's "Fantastic Four". The Council of Ricks in the cartoon show "Rick and Morty" is another parody of this story line.
Discussing his attributes in reference to his doppelgängers, Cisco tells Harry that sometimes "you're a wizard, Harry". This is a play on the line spoken by Rubeus Hagrid to Harry Potter in the 2001 film Harry Potter and the Philosopher's Stone, and the book Harry Potter and the Philosopher Stone.
Tom Cavanagh mimicked the voice and accent of Arrow's Slade Wilson, played by Manu Bennett, for Wells 2.0. Like Slade, the cyborg Wells is missing an eye.