Plot hole: Brooklyn Mission 2: After Reed and Sue confront Ben, he smashes down a fence and takes off. Only on the other side of the fence are 3 members of the Yancy Street Gang. The fence even hits these three guys and Ben runs between them. Yet, despite the fact in the previous mission, Ben took out many of their fellow gang members, including their leader, they act like they don't even see Ben. They ignore him completely as he hits them with the fence and plows between then. And then they charge at Reed and Sue to attack, and they have never even seen Reed or Sue before, nor has any of their gang.
Plot hole: In the film, it is shown that Ben is the only one knocked out by the cosmic storm, with the others conscious to get them back to Earth safely. However, in the game, things are changed so all four of them and Doom are knocked out and wake up in the hospital. They were the only five people on the station and were knocked out there, with Ben in the airlock. There would have been nobody to get them on the shuttle and take them back to Earth for a rescue. In the film, only Ben got knocked out, but by changing it in the game version, it opens up a plot hole about how they made it back to Earth safely after all being knocked out and then waking up in a hospital.
