Yeah, it had. A weapon using cased ammo has to somehow eject said cases after firing or the weapon stops working, so they couldn't cover/move the ejection port. You can see spent cases flying out when Vasquez is shooting the "real" pulse rifle prop in the vent escape scene after the operations fight. Movie mistake, I guess those were the constraints they were working with.
For the game, let's hope the developers fix this blunder.. or at least make up their minds if the new pulse rifle uses caseless or cased ammo and design it accordingly.
Outright saying it's using caseless after designing it as using cased, with an obvious and exposed AR15-style case ejecting bolt, including a case deflector behind it, is just silly.
That being said, I still have no idea how the rounds make it from the magazine all the way to the top barrel if the aforementioned bolt and firing chamber for the lower barrel are in the way...