Hole #7: I always figured the Tet didn’t know Julia had ever been OUT of the pod. Remember, at no point in the movie does a drone ever see her, except in the chaos of the fight underground. So, it was expecting her to be delivered in a pod when Jack brought her up.
As for why they put Julia back in a pod, I also assumed that the Tet wanted some means of verifying that it was her, but was doing so wirelessly. So they put two people in pods and then gave the Tet the wrong ID number for monitoring. This was probably part of the original script but cut because, while it did explain things, it also totally eliminated the surprise, for all but the most dimwitted watchers.
Hole #9: Two possibilities. Either all those other Jacks have been killed, or they’re all just going to have to accept that they can’t have Julia, and be content with their still-living Victorias. That’s just science fiction being interesting. The real problem is, there’s an extra Victoria running around who won’t get a Jack!
Of course, we don’t know what the real mixture is. Perhaps some Victorias committed suicide when the Tet went down. It would seem possible, with her character. It also seems like she’d been subtly engineered to be more posessive and protective of Jack, in order to keep him content. I mean, if we’re really looking at their setup, it’s not very charitable for her character. She’s basically a 50's-era housewife crossed with an air traffic controller, wearing heels and a fancy outfit to “work” every day just to dote over her husband’s every move.
But, you want to think about something even weirder?
There might not necessarily be a 1-to-1 ratio of Jacks to Victorias.
They might be so throughly integrated into the Tet’s heirarchy of machines and so regularly mind-wiped, that Victoria might spend some days monitoring two or three Jacks at once, and caring for whichever one manages to survive at the end of the day. Note how the flying craft Jack uses is not only interchangeable, but can easily fly itself back home unpiloted. How many hundreds of times has that happened?
On the other hand, Victoria did seem to be willing to deceive the Tet pretty easily when she needed to cover for Jack’s investigations with Julia… Not a good quality, as far as the Tet would be concerned.
Hole #6: That’s actually pretty straightforward with modern digital FX if you spend enough time monitoring the conversations and video feed. No reason an alien couldn’t do it.