Factual error: When they are running the disc from Donahue's office, the technician takes the radio to transmit their exact location. But at the beginning of the movie, they "lose transmission in the vault." There's no way a radio would work in that room.
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: Considering how much the bad guys stand to lose from Leigh's cooperation with the Feds they would have already been at her home ready to kill her long before her or her ex got there, and wouldn't need to wait for her to access the copy she made before swinging into action.