These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Designated Hero: Cavanaugh. As noted by SF Debris, 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.
Fridge Logic: 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.
Idiot Plot: 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.
Nightmare Fuel: A zombified child speaking taunts from the Big Bad to his dead father? More than a little creepy!