Plot hole: There's absolutely no reason why Kruger had to page Lee from the plane after he'd been drugged. The bad guys had no idea where Lee was until he did that and they traced the phone call. Not only did Kruger give away Lee's location, but he also gave away the only thing keeping the bad guys from killing him.
Plot hole: It's very, very convenient that the bad guys just happened to have an inside man at the FBI evidence depot ready to switch out the disc Lee made, when just hours before the bad guys didn't even know about Lee, until Donahue called for her.
Plot hole: Kruger's boss (James Caan) is in league with the bad guys. He convinces Kruger to help him protect the witness at the log cabin all in an effort to draw out Leigh from hiding and there are five bad guys at the cabin waiting for them. This of course is all a setup but what if one of those bad guys at the cabin had killed Kruger? Then Kruger's boss wouldn't know where to find Leigh and they would all be back to square one.
Plot hole: The Feds had plenty of evidence to move in on Cyrez after Leigh's encounter with Donahue especially after his admission on camera, so there's no reason the company would still be in operation as if nothing had happened. At the very least all operations would be on hold until the hearings were concluded.
Plot hole: The whole idea of copying the files to a disc (and a copy) is a pointless plot device. First of all since the information on the discs cannot be accessed outside of Cyrez the bad guys are putting an awful lot of effort into getting rid of it when all they need to do is kill Leigh. Second, if one has to be at the vault or Donahue's office to access the information then then it's no different than accessing the information on any given day of the week. All the Feds needed was a warrant to look at Donahue's files and everything in the movie could have been avoided.