In one scene, they show a map of an airport on the monitor and mention that it is a map of an "air field out near the Everglades". The map shown is clearly an overhead map of Miami International Airport.
At the end of the episode, Horatio blows up the boat by shooting an LP tank on the back with his pistol. It has been proven that you cannot blow up an LP tank by doing this. This idea was even featured on an episode of Myth Busters.
Horatio is in the Everglades talking to Yelena and he has a regular sized briefcase said to contain ten million dollars. One million dollars is about 8"x6"x13". Ten times this amount would not fit in a standard sized aluminum briefcase.
About 1/2 way into the episode, a street gang robs an armored truck by shooting it with submachine guns loaded with the "fused alloy" round. It would be impossible for a 9x19mm round to penetrate the armor of an armored truck, regardless of the composition of the bullet. There just isn't enough kinetic energy from a pistol round to do so.
When the driver's window of the armored truck is shot out, it disintegrates like regular tempered glass, i.e. the whole window fractures into small chunks. A true bullet resistant window would only show damage at the impact site and would take several shots (even armor piecing rounds).