What's the penalty for running a yellow light that just turned red?

The distinction matters more than the penalty itself - running a light that's already red is different from entering on yellow and clearing before it turns red, which is usually legal. If you cross after it's fully red, you're looking at a traffic citation that typically runs $100 - $300 depending on your location, plus points on your license that can affect your insurance rates. Some jurisdictions are stricter than others, and repeat offenses can lead to higher fines or even license suspension.