In the cutscene as Mysterio is leaving the theater, he will say "You have no chance to survive! Make your time!"

This is a reference to the infamous intro to the game Zero Wing.
Contributed by Takahashi2212
Governor's Island was meant to be included as a bonus accessible area, but due to time constraints, the area was not added. Though the island is not there, the island's name is visible on the game's map from atop the Statue of Liberty.
Contributed by gamemaster1991
Kirsten Dunst was given approval over the appearance of Mary Jane in the game. She ordered the character designers to tone down the breast size of the character in the game because they gave her over-inflated breasts.

"I got to approve the video game, the way she looks. They made her boobs gigantic. I was like, 'Tone down the boobs, please!' It was a little ridiculous." - Kirsten Dunst
Contributed by Pogue-Mahone
Some long, green feathers can be found at the location of the battle with Vulture from the first game, implying that they are left over from the fight.
Contributed by gamemaster1991