Kovich mentions an alternate reality created by a temporal incursion by a Romulan mining ship, a reference to the events of Star Trek (2009). This is also the first Star Trek episode to mention or include any characters from the alternate reality.
Carl's newspaper has the name "Star Dispatch" on the masthead. That's the same name of the paper in the The City on the Edge of Forever (1967).
Lt. Cmdr. Stamets mentioned the prefix code to get a backdoor into the other Federation ship's sensor array. This is a reference to Star Trek II: The Wrath of Khan (1982), where Kirk and the crew of the Enterprise used the prefix code as a backdoor to take over the Reliant's shield systems.
An aerial view of Georgiou and Burnham walking through the wilderness in the show shows a long trail of footprints behind them. This is very reminiscent of the first episode of the show where the prime Georgiou and Burnham walked alone in a desert.
Lt. Cmdr. Yor is seen wearing the uniform style used in the first 2 seasons of Star Trek: The Next Generation (1987). During filming, the unknown stand-in who played the character was mistakenly outfitted with the communicator badge designed for Star Trek: Generations (1994) (also used in later season of Star Trek: Deep Space Nine (1993) and all of Star Trek: Voyager (1995)), which featured a hollow gold trapezoid behind the Starfleet delta, rather than the communicator badge with the gold oval, as would have been appropriate to the uniform style. Fans on social media noticed the discrepancy when preview images for the episode were released and the badge was quickly digitally replaced before the episode ever streamed.