While cutting to Wolverine's scene at the airport, the overhead announcer can be heard stating "flight 181 to Madripoor now boarding at gate x-23". X-23 is reference to a character in the comics who is a clone derived from Wolverine.
The X-Men were fighting the Inner Circle at the beginning of the episode. Mastermind is the shadowed villain laughing when Jean dies.
Beast is shown to be respected and accept like a regular teacher; no student makes fun of his mutant status.
The airport announcement, "Flight 181 to Madripoor at gate X-23." makes three references to the X-Men comic book. Flight 181 refers to X-Men Vol 1 issue 181, "Young Dragons in Love" in which the X-Men spend most of the time in the air with two dragons. Madripoor is a crime based country which Wolverine has had many run ins with. And X-23 is a female clone of Wolverine.