Because it simply cannot understand human nature. The Tet is an artificial life form, which can anticipate human responses to certain extents, but it can never comprehend the emotions behind them. It mistakenly thought it had learned all about humans from studying the data aboard the Odyssey.
That's why it took Jack Harper and cloned him by the thousands: with no memories of his earlier life, it expected Jack could be programmed to be the perfect weapon to wage its war. By thinking it understood him, it thought it could have absolute control over him. Which was true during the war, when the army of Jacks nearly wiped out humanity. The Tet probably assumed that the remaining people would fear the sight of him forever, and never reach out to any of the Jacks remaining on Earth as caretakers. So the Tet could easily fool Jack into thinking that the humans in disguise were remaining Scavs.
Its flaw was that it did not expect Jack to retain one vital memory, one of the love for his wife. It was so deeply rooted in his emotional being that it would resurface in every clone of Jack, given enough time and opportunity (notice that Jack from Tower 52 freezes temporarily at the sight of Julia, implying he remembers her as well). Even more so, the capacity to love also extends to all things from the Earth, its environment, music and culture. Despite having no memories, Jack still feels that Earth is his home. The Tet did not realize that a love for the Earth is so deeply rooted in humanity that it cannot simply be 'erased' (according to Victory from Tower 52, Jack 52 also had a similar desire to stay on Earth).
So the flaw in the Tet's plan started to backfire when General Beach (Morgan Freeman) noticed Jack 49 picking up a book, and saw him defending the people in the pods against the drone; this convinced him that despite everything, Jack had retained his humanity. The Tet never knew that Jack was cooperating with the other humans, and didn't expect him to. Even when Jack learned the truth about the Scavs and the Tet, the Tet was convinced Jack was no longer human, and thought it could keep his allegiance by promising him things. Nor did the Tet understand the true meaning of death. It simply thinks that all humans have an instinctive urge to stay alive, and does not calculate that Jack may sacrifice himself for Earth and its people. Even when the Tet seems to suspect something is wrong as Jack proceeds into the object's interior, and suspects he might be lying, it ultimately accepts as true his genuine desire for humanity to survive.
As for the Tet not suspecting that Jack may be carrying the drones' missing fuel cells: it had ordered the drones to follow Jack's trail to the humans' secret hide-out, and may have assumed that the drones would wipe out the entire human resistance, along with the fuel cells. Again, since Tet did not expect Jack to work with the humans, it did not know that Jack had helped them defeat the drones and obtained the fuel cells.