Plot hole: While planting the suicide gear in the bathroom before Buckley comes in, Cooper tells Josh to tie the rope into a noose as they go to hide in the shower. Josh replies that he doesn't even know how to tie a noose. He must be a quick study, because in the 45 seconds or so that it would have taken Buckley to relieve himself and wash his hands, Josh has tied a perfect noose.
Plot hole: In his mad dash from the security guard at the Mental Health Facility, Cooper drops about 90% of the file folders he had taken. Yet he somehow manages to hold onto the files for the main people they were photographing earlier in the film. You can argue that he guarded those files better, but then why bother grabbing so many "expendable" files in the first place? It just seems like a cheap plot device.