At the beginning of the episode, when Felicity tells Ray why Earth-XNazis have taken over S.T.A.R. Labs, the last point Felicity says is "and they have a giant robot". Ray replies by saying "I've actually fought one of those." He then explains that in addition to shrinking, his suit enlarges. This most likely refers to the events of "Leviathan", where Ray enlarges his suit, and himself, to enormous proportions to battle Vandal Savage's robot.
While stopping the surgical blade, Ray quips "Mitts off Mengele". This is a reference to Josef Mengele, the Nazi doctor nicknamed Angel of Deathdue to his various inhuman experiments on the victims at the Auschwitz concentration camp.
There was a deleted scene in which Harry and Eobard met. Thawne intended to vibrate his hand through Harry's chest, but Harry filled his body with nanorobots that would reject contact with any speedster, since Harry did not want a speedster to harm him anymore. In this scene Harry calls Thawne an alternate version of him even if Harry disliked that his fellow Team Flash members referred to Thawne as Earth-1 Wells.
When Diggle officiates Iris and Barry's wedding at the end of the episode, neither Barry nor Iris says "I do".
This is ironic, considering that when Barry's future daughter approached him immediately before he and Iris tried having their wedding earlier in "Crisis on Earth-X, Part 1" (prior to the Earth-X invasion), before she left, in her nervousness due to meeting her father for the first time, Nora told him "Good luck up there. Remember to say 'I do'."