Deleted Scene: In the fourth episode, there was a scene where Harry meets Thawne. Thawne offers Harry a place in the New Reich because of his intelligence, Harry of course refuse. Thawne then tries to kill him via his vibrating hand only for it to be repelled; after his encounters with Zoom and Savitar, Harry injected his body with millions of nanobots programmed to attack any foreign cells trying to enter his system, after which Thawne quickly leaves.
Dueling Works: With Justice League (2017), DC's other big Avengers, Assemble! event of 2017, which premiered two weeks before the crossover between the CW shows. Even with the controversial elements of the crossover (such as the emphasis on relationship drama in Part 2 and the despised ending), most generally agree that the crossover overall was better than Justice League.
Executive Meddling: Apparently it was Greg Berlanti's idea to end the crossover with the now infamous double wedding. Given what happened in the subsequent "The Flash" episode it seems like the writers would've rather not ended it that way.
People theorized that either Tommy Merlyn or Roy Harper was Earth-X Prometheus, since Colin Donnell was reported to be seen on set and Colton Haynes tweeted he would be returning to Arrow. It turned out he was the former.
Ever since Victor Garber announced he was planning to go back to Broadway, it was teased that Martin Stein will be retiring. And because of Retirony, many people correctly guessed that he would die in the crossover instead of actual retirement.
Leigh improvised the "sassy assassin" bit during the conversation Alex and Kara had right afterwards.
Troubled Production: A more mild example than most, but by all accounts this was not an easy event to produce, trying to coordinate the event around each show's schedule was nightmare; which is why the Legends were left out of the next crossover Elseworlds.
Katie Cassidy was suppose to show up in some capacity, but then her father died so her planned appearance was written out so she could go to his funeral. The Flash episode, "Fury Rogue" revealed she would've been cast as Siren X, the New Reichsmen's answer to the Black Canary. Siren X makes a later appearance; she was Oliver-X's ex-lover and pissed that the Earth-1 heroes killed him.
Marc Guggenheim tried to get this released as a single movie instead of a crossover spread out over four shows, including new material. But "union rules regarding credit" put on kibosh on the plans.