Speaking more specifically to the topic title, "Darkest Hour: What am I to make of...", I could go on for a while if I had the book right in front of me. I found many inconsistencies and some flat-out contradictions of continuity in "Darkest Hour." Here are a couple off the top of my head:
In a sidebar, Jane is depicted as wearing an amulet surrounding her with a high-rating mana void. I was not able to find any explanation as to why she was doing this. I can think of a few, but it's a weird thing to leave totally unexplained.
When the team is meeting their contact in Hamburg at a anti-NEEC rally the name given for the location of the rally is very obviously a different place than the description and map given for the location. Thirty seconds with Google Earth showed me that, so what excuse does the author have? I guess you could argue that this is a minor thing but these days all of my players are sitting at the table with laptops and if I mention a real-world location someone in my group has it up on Google Maps/Earth immediately, which means errors like this don't slide like they used to.
In the section entitled "Grabbing the Disc" it specifically says in the Behind the Scenes section that the Aztechnology agents assisting the police with the investigation of Hermann Meyer's murder are positive that no one from Aztechnology was involved in the murder. The text goes on to say that the murder was perpetrated by a shadowrunner from Bogota who was instructed to make it look like an Aztechnology blood mage did it, but the text fails to identify who the Johnson was. Then in the final section called "Finding Lost Treasure" I'm reading the description of Captain Herrera, the Aztechnology commander at the Bosnian pyramid site, and it specifically says that it was she who came up with the "idea to get the disc from Meyer." So, what, is Cpt. Herrera independently contracting shadowrunners and going behind the backs of her Aztechnology superiors? I think not, especially given the other line from her description which says she is "...loyal to Aztechnology." In fact, there is no other evidence that I can find that would indicate that anyone from Aztechnology even knows the disc exists; the reason given for there being an Aztechnology expedition at the Bosnian pyramids is that the pyramids are so much like Meso-American pyramids. So what are we supposed to make of this contradiction?
Frankly, the overall impression given by "Darkest Hour" is one of organizational chaos. My understanding of the staff turnover at CGL leads me to believe that the transition from the original DotA author, who no longer works for CGL, and the new author is mostly to blame for the problems. A new author brought in to finish someone else's work is inevitably going to miss details and lead to continuity errors. The real shame is that none of these things got caught in the playtesting, proofreading and editing process. You'd think that someone along that chain would have picked up on these mistakes.