Why did Wheel Cleaner leave my tires brown

Sometimes this happens if the tires aren't completely rinsed off after cleaning.  Since it's a wheel and tire cleaner, it's simply working it's magic to bring all the dirt/grime out of the tire and bringing it to the surface.

The best way to fix this would be to use a stiff bristle brush. I would suggest a stiff bristle brush like this:
https://www.amazon.com/gp/product/B000OCH8BI/

-Spray the Wheel Cleaner onto the tires, then since your tires are already brown, I would suggest doing at least 2 rounds of hard scrubbing/rinsing with water, spray the cleaner again, scrubbing/rinsing, with the stiff bristle brush. This should get rid of all the brown parts.

The next step would be to thoroughly dry your tires, then hit them with our Tire Shine to rejuvenate and keep them protected.