Plot hole: The FBI in the movie has the ability to "blackhole" an IP address, which makes that computer unavailable to the internet. If they can blackhole the computer acting as the web server, they could also blackhole the computer acting as the name server (DNS), thereby taking down the web site and preventing additional users from connecting.
Continuity mistake: The skull on the Killwithme website is an x-ray of Owen's father's head. In the movie, it was mentioned that the glasses were found on the roof by an employee, and was sold on some website. Why would the x-ray have the glasses on the face of the skull if they were not with the corpse?
Revealing mistake: At the beginning, Griffin sits back on his chair after getting information about the first hacker who attacked their computer. He's about to put his hand on a trackball, and you can see for a second a badly covered Logitech's logo (they have left some characteristic details); the model is a Logitech TrackMan.
Continuity mistake: When the detective and police arrive at Mrs. Miller's boat, you can see a group of reporters in front of her door. The woman with blond hair changes her dictaphone to a microphone between shots (she also moves between scenes from just in front of the door to one side and to a few feet away from the doors). And the whole group of reporters changes its position between shots.