Every structure in the universe is built from leftovers. Particle physics symmetries say the Big Bang should have produced baryons and antibaryons in equal numbers, followed by mutual annihilation into radiation; instead, roughly one baryon per billion photons survived, the asymmetry eta_B near 6 x 10^-10 from which all matter descends. Sakharov catalogued what any explanation requires, baryon number violation, CP violation, and departure from equilibrium (Sakharov 1967), and the Standard Model formally contains all three.
It contains them at the wrong sizes. The CKM matrix's CP violation amounts to an effective magnitude near 10^-20, eighteen orders short of what the observed asymmetry requires; the Standard Model's sphaleron processes violate baryon number but operate too gently in the smooth thermal early universe; and the electroweak transition, once hoped to supply the out-of-equilibrium stage, turned out to be a crossover rather than the violent first-order transition baryogenesis needs (Cohen et al. 1993). The standard responses all import new physics, leptogenesis with heavy right-handed neutrinos, supersymmetric baryogenesis, GUT-scale mechanisms, each unconfirmed by experiment and most untestable at accessible energies.
The standing is one of the deepest open problems in fundamental physics: the universe's matter content has no accepted origin, and every proposed origin lives beyond the Standard Model's experimental reach.