I misunderstood this during Bibi's presentation too. The half ton of nuclear material was documentation about their nuclear program NOT half a ton of enriched uranium. It was very thorough and seemingly all inclusive though.
I'm liking the theory that IRGC supplied all that material to (either us or) Israel. Makes more sense than that Israel actually accumulated all that on their own. It wouldn't surprise me if it was not supplied to us (and we have the originals) and that Bibi was really displaying the copies that he spoke of. Hence, the originals being safe in another place.