I had this problem too, tons of black smoke, ruined the primary cat. It was because of my MAF fouling. Although this was with a bad supercharger and everything else stock. Didn't get a CEL for several miles. It may take anyhwere from 1 to hundreds before a CEL comes on.
Warranty should cover this under 60k and 5 yrs for the MAF (Mass Air Flow sensor), located on the intake. I think its under 80k for the cat if it needs replacement.
Edit** Caution, use method carefully and at your own risk. Check your connections to the throttle body. If there is an air leak, your MAF must be reading less air, so it'll bog the engine and will even cut off while driving. You can get a can of throttle body cleaner at Walmart, its red and white. You CAN use it with the engine running. Just let it warm up, spray where the throtlle body and silicon tubing meet. The engine should bog a bit if there IS a leak, if it doesn't, then check any other (if there is) silicon tubing, between throttle body and MAF. I should mention that you DO NOT spray it before the supercharger or MAF. If there is/are leaks, just tighten the loose connections.
Scion tC 2005 flint mica TRD Supercharged-died
Scion tC 2009 blue ribbon metallic no longer S-Charged