* DesignatedHero: Cavanaugh. As noted by WebSite/SFDebris, in the pilot alone, he bugs the homes of his fellow team-members without permission, has the team implanted with tracking devices, routinely roughs up anyone who questions why he is violating their civil liberties and uses his firearm as both a lockpick and television remote.
** It should be noted that bugging the homes of his team-members is actually following Threshold protocol, ''everyone'' violates civil rights, and shooting the television saved the lives of his teammates.
* FridgeLogic: What exactly was the threat of the North Koreans in the pilot? The US team was already on the scene and securing the vessel? Not to mentioned the reason to destroy the vessel was to stop it falling into their hands? How? It was a US vessel, with US military personnel onboard... to do so would have been an unprovocated ''act of war''.
** For that matter, what in the name of Kim Il-Sung was a North Korean submarine doing in the North Atlantic?
** And they explicitly said it was a ''Kilo''-class sub. An American ''Los Angeles'' class would consider a ''Kilo'' target practice.
* HilariousInHindsight: Creator/CarlaGugino would go on to play a UFO researcher in ''Film/RaceToWitchMountain'', which also stars Ciaran Hinds as a [[TheMenInBlack MIB]]-type character akin to Dr Caffrey.
* IdiotPlot: Why would you put a contingency planner on direct control? Why would you leave her there when every single decision she makes back-fires horribly?
** You put her there because it's her plan and "no plan survives contact with the enemy," so have her be there to hopefully deal with every ''contingency''. Keep her there because, despite her failures, she's still the main reason things aren't even worse - especially when failures come down to things out of their hands, like lack of manpower or resources, or getting strong-armed from above.
* NightmareFuel: A zombified child speaking taunts from the BigBad to his dead father? More than a little creepy!
* WholePlotReference: TheWarOnTerror [[RecycledInSpace with alien invasion]]! All the shady moves Threshold does, especially the indefinite detention without court or any infromation, are potrayed with their full moral ambiguity.