As Michael is walking towards the pay phone to make his 'setup' call, there are two ladies who walk behind him while talking to each other. One in a white dress, the other in shorts and green shirt. When Michael and Fiona are watching for the response to the call, those same two ladies walk past the agent, and now they're apparently strangers.
As Michael and Sam depart the lower decks, Michael has a gun in his hand. As they exit the upper his hand is empty but when they cross the gangway it is in his hand again.
The conversations in the intro are different from the original conversations.
Michael and Nate are discussing Nate getting him and his Mother to Ft. Lauderdale and mentions that he had the Charger windshield fixed. In a previous shot Michael and Fiona are scouting the Episode Villian's base in the Charger. Almost no time has passed between the two scenes.
Michael is wearing his jacket when Phillip is shot, and Michael gets spattered with blood. Later, when Michael removes his jacket, there is blood on his shirt where there shouldn't be any, because the jacket was covering it.
When Michael goes in the water to lay the sticky mine, he is wearing a dry suit. A dry suit is designed for cold water diving in waters between 30-60 degrees F. It's wholly unnecessary for south Florida waters which are usually a quite comfortable 75-85 degrees F and is actually a hindrance in special ops/UDT work due to the suit being very baggie and causing excessive drag.
As Michael prepares to climb onto the boat he throws a three prong grapple hook over a railing with plastic covers on the tines, the audio has a metallic clink as it connects.
At the very end when Michael is driving in the Caddy via the Onstar in the Florida Keys he stops behind the 18 Wheeler, he is going the wrong direction on the Seven Mile Bridge. If he was leaving Miami, the "Old Flaglar" Seven Mile Bridge would be on his right, but it is on the Left. The means he was going toward Marathon (and Miami) when the last part was filmed.