On the exterior shot of the building Roberto da Costa is being held by the Friends of Humanity, there is a missing person poster on a pole. The person on the poster is Marrow, a member of the X-Men in the comics in the late '90s / early '00s.
When Beast hijacks the Sentinel he paraphrases the last line of Casablanca (1942): "Louis, I think this is the beginning of a beautiful friendship."
After Cyclops' optic blast blows out the windows of the Friends of Humanity HQ, the front page of the Daily Bugle floats by in the air. Its headline says "Benetton's Mutant Fashion Show" with a picture of four mutants that have been members of the X-Men on different points in the comics; Banshee, Dust, Stacy X, and Maggot.
Jean calls Gambit by his real name, which the team never did in the last series; except for Rogue. Otherwise, Wolverine would nickname him "Cajun" for his background.
When Jubilee questions Roberto about his powers, she asks if he can "Shoot gold balls from your body? That'd be weird." This is a reference to Fabio Medina aka Goldballs / Egg, an X-Men ally in the comics who has the power to produce gold balls of different sizes from his body.