I know exactly what you mean. But I don't call these "plot holes". They are technical gaps. Huge ones, but nothing that will impact the story or the wrap up for those who are not knowledgeable about US Navy subs and nuclear missiles.
Plot holes are things like:
-What was the SEALs' real mission?
-Why didn't the SEALs help the crew when it became apparent the intent was to be rid of them in order to preserve all secrecy?
-Why have "THEY" not killed the woman who designed the cloaking device? Why do they let her keep trying to gather more evidence and information?
And there are more along this line.
From the three episodes I watched I got the impression that info was part of the story arc that would be revealed to as to story developed. I kinda expected we wouldn’t see that part of the story until they developed some of what’s going on. I see their mission and their actions in the beginning as a couple of the clues to the conspiracy that they will introduce at the story arc progressed. I don’t consider the SEAL’s story a plot hole.
As for the woman in DC (Sinclair?), I see here as one the protagonists to advance the story in DC. I think the idea is that she’s supposed to be prominent enough that having her whacked would draw too much attention. I think that’s why she’s not just a lobbyist but also the daughter of a big wig in the defense industry.
I believe both of these are necessary in order to advance the plot line. I don’t think these are plot holes...but I've been wrong before.
I see exploding a nuke 100 miles of the eastern seaboard, in one of busiest shipping lanes on the planet, with no damage, casualties, or contamination as a huge hole...and the one I’m having the most trouble with. I could overlook everything else if the story is good enough but nuke pushes it over the edge.
My 2¢ FWIW.
Since it costs 1.66¢ to produce a penny, my 2¢ worth is really 3.32¢ worth. That 3.32¢ is my own and not the 3.32¢ of DIRECTV, Dish, or anyone else for that matter.