Why was the Tet so full of clones so close to victory? You'd think at that stage it'd be scaling down production.
The number of clones in the Tet must have amounted to thousands, and I'd guess it took quite a lot of resources to grow them.
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There is no reason to assume the Tet was near completing its project. If the Tet were a self-replicating machine, a basic strategy would be to mine energy and other resources from Earth to make as many Tets as possible. Fifty years isn't nearly enough time to sift all the deuterium out of Earth's oceans, or to strip mine the planet for metals, fissile materials and whatever else an agent of a Kardashev type 1 civilization might find useful.
The extra Jacks and Vikas might be there for contingencies. The scavs were still mounting significant resistance. The Tet could not be completely sure that a large number of clones would not be needed suddenly, so it would be prudent to have them on hand.
We don't know how many Jacks and Vikas are deployed on Earth. A large number of replacement clones might need to be baking at any given time to deal with voluntary "retirements" and involuntary ones due to scav attacks.
Since the Tet is an automated system that has been using the Earth's own resources to power itself (and as a source of genetic material to make soldier clones) and since the "scavs" are proving annoyingly persistent as a guerilla force, I think we can reasonably assume that Sally would consider creating and storing clones on case of a resurgence of resistance to be worthwhile activity.
Heck, It's not like it costs them anything.
On the other hand it might just be one of the movie's many, many incomprehensible plot holes.