^AHAHAHA I did the same thing.
The article did touch on some of the same things I pointed out. Main passages here
The story of the Impossible Girl also comes to its conclusion, and it’s been a fine old ride. The very fact it resulted in that augmented crazy clips package justifies the whole exercise, before we even get going on the explanation. The concept of Clara splintered in time (I’ve seen City of Death, I know the lingo), and interacting with every incarnation of the Doctor is grand. To have something that tinkers with the everythingness of Doctor Who is exactly what we need in this year of years. And because of that, it works as a first pass. But look at it for a moment longer, and it falls to bits.
Why, if Clara’s been bobbing around the Doctor’s time stream, didn’t he recognise her when they met sans Dalek casing in The Snowmen? Readers, I’ve given this a bit of thought. I guess the line “But he almost never hears me” covers that. But it’s a flip-floppy piece of writing. The Time Lord’s never aware of Clara, except for those moments when he is? I’m also at a loss to work out what the Great Intelligence is actually up to when he inserts himself into the montage. Are we to read this as him continually killing the Doctor? Or just standing around all day looking tough (which must be very wearing on the nerves)? Also, how is Clara thwarting his efforts? Does her presence somehow boot him out of the time stream? Do they wrestle? Plus, where exactly are she and the Doctor at the end of the episode? And, hang on, this has just occurred to me – how come Clara’s suspicious of River’s grave? She states she knows the prof isn’t dead, but neither is the Doctor and no one’s querying his resting place.
Normally I’m not sure how much these details matter. Particularly in a story that’s about to skewer our understanding of Doctor Who history. But when so much screen time is also devoted to plot mechanics, it begs you to make a closer inspection.
Like myself and most people, we found TNOTD really riveting and engaging the first watch through. They were throwing some heavy shit at us and it all sounded pretty good. However upon rewatches and thinking about the episode logically, you realize it's full of holes and doesn't make any sense. It's sort of like Moffat is the Master and he's hypnotized everyone in the fandom. Doctor Who series 3 "The Sound of Drums" style. Don't know what he's talking about but it sounded good.