I think it could be one of a bunch of things. In the game, just picking up the crystals may have automatically acquired them. Think of how you usually pick up loot in games, I don't care if it's VR they probably wouldn't bother adding too many unnecessary steps to this in a shooter.
On the other hand, if what he just did accidentally is generally how you looted the crystals in the game, then it could have been the "elemental" bit of things. The game seemed like a scifi FPS, so the crystals dropped there were probably all like this one. Not attuned to elements that'd make them useful for particular types of magic.
Then there's always this option. He didn't think to try treating the crystals as if he was still in the game, because he's not still in the game. Sometimes you miss "obvious" things because you think too hard about them, and this could also tie into why the title calls him stupid but I think that's probably just related to the can't use magic thing since they explained that with part of this world's setting. He's a human being, even geniuses make mistakes or miss things.
Naturally the author could just be less than an amazing writer as well. If this series follows the usual pattern for how it got picked up, it was being written by some amateur online and then managed to get published as a light novel series before finally getting adapted into the manga. Popularity/success and objective quality aren't necessarily at 1:1 ratios in any entertainment media.