In this episode, on the other side, they don't know who Batman is, and instead Batman is known as Mantis. But in the season finale of Season 2, when Olivia, and William Bell are shooting at the Fringe Division from the other side, right before they switch Olivia's, there is a movie theater across the street with a lot of different movie titles, one of which is titled 'Superman VS Batman 2'.
Lincoln fires his Glock at the sniper and when he reloads, he works the slide to chamber a round. If the pistol had been empty the slide would have been locked back, and if it was not empty a live round would have been ejected. In neither case would he have been required to rack the slide.
In the Alt Universe, towards the end of the episode, when Astrid enters Broyles office she addresses him as "Agent Broyles." In the Alt Universe he is Col. Broyles.
Not only do the team enter a bio-hazardous area with no medical protection (as they do more often than not), the lead agents chase the suspect with handguns and no body protection, while the rank and file trail them, wearing helmets and flak jackets, and carrying automatic weapons.