Welcome to the site!
Not real familiar with the newer model years - but the only place I'm aware of where the two fluids could cross-contaminate is at the tranny fluid cooler located in the radiator.
If you inspect the radiator closely, you should see two small lines entering one of the reservoirs at the ends of the radiator. Offhand, if you used a chemical for the flush, wondering if the chemical didn't attack the fluid cooler metal??? If you're mechanically inclined, you can pull the radiator and most any radiator shop should be able to get you back in business.
