Things you didn't realise were a reference
I'll just get straight to my examples
In Marvel Vs Capcom Infinite, every character has a level 3 super due to how the stone system works, therefore any character returning from Marvel 3 who didn't have a level 3 was given one like Spider-Man, Nova, or in this case Spencer. His Level 3 just involves him slapping the opponent and placing a grenade next to their head and swinging away, pretty lame and one of the weaker supers in the game. Years later I watch a video about the Bionic Commando game that this version of spencer is based on and see that this exact scene is lifted from the conclusion of one of the boss fights. It doesnt make the super any better but does at least make it more interesting.
On the Marvel side of things though is Iron Man, during his DEATHBATTLE he had VS Lex Luthor. At the Climax of the fight he equips his at the time very new Endo Sym armor, makes a very cool statements on how "I'm not playing God. All this time, I've been playing Human." theres a Sawano drop and he kicks Luthors ass, is super dope. I wasn't until years later that i found out that this wasn't just a kinda cheesy but cool line written for that fight, but a quote lifted almost verbatim from the Superior Iron Man comic that suit is from (also he says it after curing daredevil of his blindness), only difference being that its directed at Lex Luthor.
Any times you didnt realise something kinda big was a reference