During Oliver's final rooftop fight, he is knocked off his feet, and his bow lands about a meter away from him. In the next instant, he sits up, and his bow is back in his hand.
Earth-16 Oliver Queen believed Sara to be dead on the Gambit and they had never met prior. Whereas in Star City 2046, Oliver knew Sarah survived and referenced his conversation with Ray Palmer in Pilot, Part 1.
Careful: Sara says «one of the benefits of parallel Earths». It would appear that Earth-16 in this episode is not in the same universe as Star CIty 2046 in the pilot episode mentioned, but is instead in a parallel universe.
The Legion returned to the future with their ship. Mon-El and Winn Schott were seen inside the ship together, before returning to the future.
Joker (Earth-89) was said to be captured by Batman (Earth-89) and is also confirmed to be the same Batman and Joker from the 1989 film, Batman. However, in the film, Batman killed the Joker.
Just before they evacuate Jonathan from Argo, Alura says "thank god" when she's relieved to see that Lois and Clark are okay. As a Kryptonian, she surely would refer to their god by name and use the phrase "thank Rao".
About 10 minutes in at the beginning of the Central City segment, the Flash calls Harbinger / Lyla Michaels «Dinah» instead of «Lyla».