When Loki tries to use the Tesseract to facilitate his escape in Episode 1 of “Loki,” he finds its former power useless. He even sees that the bureaucrats at the TVA use the excess Infinity Stones that end up in their office as paperweights. Director Kate Herron told The Hollywood Reporter that this was done to show that “the TVA is not only a force to be reckoned with, but it’s also completely new terrain for the MCU. This is a new space with new rules and new power.”
However, Reddit user Usagizero thinks there’s a deeper, more canonical answer for the inert Infinity Stones that Loki encounters in the TVA. The reason that the Infinity Stones have no power may not necessarily be because the TVA is an all-powerful entity, but because in the comics, “the Infinity gems only have power in the universe/reality they come from.” Usagizero added that they believe the stones are “powerless” outside that universe.
Usagizero notes that there are even official Marvel comics in which villains have acquired Infinity Stones outside of their original dimension, only to find that they are nonfunctional. Additionally, they mentioned one storyline involving Loki that depicts the mining of significant quantities of Infinity Stones. Because the TVA exists in its own reality outside of the normal dimensions, Infinity Stones no longer pose a threat when they end up there.