The heroes will mention Lilith in fight dialogue even against Vampyres and Turned Hydra, whom AREN'T loyal to her.
The first time you go to "train" to upgrade an ability, you can chat with Blade. While chatting, you can see a few team members training in the background. You can see Nico, Magik and even Ghost Rider is there training. After you upgrade the ability and get control back, Ghost Rider is gone and Doctor Strange is now in the training area.
The Hunter is invited by Nico to watch a movie. The movie Nico chooses is a western, which can be seen on the screen. Nico then says to The Hunter "The glowing briefcase is a metaphor." This is a reference to the movie Pulp Fiction, which is not a Western and obviously not the movie they are watching.
Some copies of the game will constantly present an error message every time a turn ends during a mission. This glitch only activates upon starting the mission to rescue Spider-Man from Fallen Venom.