I thought that there were only six Infinity Stones. Exactly six. I didn't pause and count them, but it sure looked like more than six in Casey's desk drawer, plus Casey said that they had a lot of them and some guys use them for paperweights. So there's even more, somewhere.
So... there are only six in our universe, but this show (or at least the TVA) exists outside of (or beyond) our universe? Something like that?
Here's how I interpret the multiples of Infinity Stones - They're all from pruned branch timelines, like the Tesseract that Loki stole in Endgame. The branched timelines were clipped and reset with their time grenade charges.
It kinda makes sense that there would be more Infinity Stones at the TVA considering the power they hold, tons of nefarious beings would try to take them and cause chaos, which could incite branch timelines which would need to be pruned and reset. So as we see in the drawer, there are about six (red) Reality Stones, and if the Dark Elves were willing to destroy Asgard to get them, you can imagine how far other beings would go to get them to try and use them to recreate the universe.
There are about four (purple) Power Stones, and being the most physically destructive stone, a lot of war mongering villains would be after them, which is probably why in the prime MCU timeline, the Nova Corps were best trusted to keep it safe (though that did not stop Thanos, but then again, that was *supposed* to happen). There are about six (green) Time Stones, and of course, that would need to be watched carefully because of how easily it could alter the timeline and create multiverses easily (as Mordo warned in the Doctor Strange film).
There's one (blue) Space Stone, which is interesting that it seems like there aren't more of them, but it's probably one of the weaker stones in terms of it's power to alter the timelines since it just displaces people in the three dimensional space within the universe, but there might be more as paperweights around the TVA offices. And there are two (yellow) Mind Stones, which I've seen a lot of folks confuse for the Soul Stone, but the color brightness is a bit dark in the drawer, and the stone itself is seen to be quite larger than the others, which is how the Mind Stone looked in Infinity War (and Endgame) when it was pulled out of Vision's head. Granted, the stones could morph their shape to fit into the gauntlets, but it was always bigger than the other five stones, so I'm 99% certain those two bigger Infinity Stones are Mind Stones.
It also makes sense that there are no Soul Stones considering how difficult they are to obtain, though there are some stones in the credits of the show, and I hadn't seen if there were any orange Soul Stones in there yet. But yeah, hopefully that makes sense. The extra stones are just from branch timelines, so they were taken out of the Sacred Timeline, but because they're in a place outside of their home universe, they're powerless (an idea I recall being mentioned during the 90s Marvel VS DC Comics, where Darkseid came upon the Infinity Gauntlet (with all the Infinity Gems) and he tried using it, but it didn't work in the DC Universe because they weren't in their home universe - very clever writing.
-Marc.