Before the big reveal the 2099 Alchemax CEO is himself, Peter makes one nice remark :
Spider-Man: So this is where you make the big reveal, and I say, Holy cow! Norman Osborn or the Kingpin or Jonah Jameson! C'mon PLEASE be Jameson
Speaking of Jameson, on the third Newspaper which details J. Jonah Jameson, the normal timeline says "J. Jonah Jameson in tight race for Mayor.", in the other timeline, it's "J. Jonah Jameson buys mare to race.". In another, Hammerhead is a hat salesmen in the Alchemax Timeline.
Present day Spider-man mocking Miguel and the 2099 future's general use of the word "Shock".
Peter trashes the robotics lab to get rid of the robot sentries attacking Miguel in 2099.
Amazing Spider-Man: O'Hara! There's nothing left here to trash! You still there?
[Robot sentries disappear]
Spider-Man 2099: Yeah. For the most part.
Amazing Spider-Man: Did they turn into something else? Like, I don't know, kittens?