When Arnett's casket is exhumed and taken to Ducky for reexamination, it is in pristine showroom condition. This is impossible for a casket that has been buried, there should be some sign of dirt or water stains on it after being buried for several weeks..
It's established that Lt. Arnett worked at the Pentagon and lived on the Pautuxent River NAS (in southern Maryland). It's also said that he takes a train to the Pentagon every day. There are no commuter trains that go from southern Maryland to the Pentagon.
The train trip starting from Shady Grove which McGee describes as a 55-minute ride takes precisely 34 minutes.
When Matt Burns arrives at the bridge over Rock Creek, the sun is high in the sky. However, the time in the story is supposed to be 6:00 AM.
Near the end of the episode when DiNozzo and McGee are confronting Will Sutton, McGee moves his jacket behind his back revealing his pistol. He also reveals his microphone antenna sticking out of his back pocket.
In the prologue, when the camera pans back from Matt Burns on the bridge, a mountain is seen on the horizon. There are no such mountains in the District of Columbia.
The path that Lt. Arnett went to work (and where he met Sutton) is completely illogical. He took a train to the Pentagon (where he worked), then went to the Bethesda Metro (a 30-minute drive on a good day), then took the Red & Yellow line trains back to the Pentagon.
When Tony and McGee are running from the dogs in the impound lot. Instead of trying to make it back to the gate they first climbed over. McGee could have simply hopped the fence to his left which was close to the cars he was running on top of. It clearly leads to the street.
ln the scene in which Ducky learns from the metro M.E.that Burns' death has been ruled a homicide, he tells Gibbs, and then says "and what does that infer?" Ducky, being highly educated and extremely erudite, would know that the correct word is "imply", not "infer"
Of course he could also have said, "what do you infer from that?"
Ducky, when comparing the other cases to the current one, said "Do the other cases infer that they may be linked?" The proper word is "imply".