As Feynman said: It is like a chess game. If you are in a corner with only a few pieces involved, you can work out exactly what is going to happen, and you can always do that when there are only a few pieces. And yet in the real game there are so many pieces that you can’t figure out what is going to happen ... There is such a lot in the world. There is so much distance between the fundamental rules and the final phenomena that it is almost unbelievable that the final variety of phenomena can come from such a steady operation of such simple rules.
The scientists that mrjangles derides, who "claim to understand the structure of the universe", sound to me like physicists claiming they know the base rules of the game. (I'll set aside that nobody has cracked, say, quantum gravity yet).
When we talk about the puzzling mysteries of the structure of glasses, or superconductivity, or turbulence, or so on -- most of those aren't a matter of a lack of understanding of the base rules of the universe, but rather their consequences when applied to a big system with a lot of parts. That's knowing the rules for how rooks work, but being surprised when your opponent captures your queen with one.