On his business card, Roberto DaCosta has his address as 1 Claremont Avenue, Rio De Janeiro, Brazil. The street name was an homage to Chris Claremont, writer of many of the X-Men comics' storylines.
The hangar at the X-Men's secret headquarters in Muir Island has a motorcycle resembling the Wolverine Mutant Cycle toy released by Toy Biz in 1991.
When Morph turns into the Hulk they say, "Morph Smash!" a parody on the Hulk's famous catchphrase, "Hulk Smash"
It's worth noting that Magneto could have taken this method YEARS ago as an easy way to kill humanity and pull a Noah's ark for mutants. But the long term damage is what deterred him. Unfortunately Bastion finally drove him over the edge, which is why Magneto has utterly given up on everything. He's plenty willing to just perform genocide now. Showing that villains that push anti-heroes too far end up screwing things up WORSE.
Sunspot is seen wearing his X-Men uniform for the first time in the series.