CSS & JS minification operates on cached CSS and JS files only. Once Cloudflare returns a cache HIT for the file it will be returned to browsers in minified form. This allows us to deliver a more complete minification result. If you need to enable or disable minification for CSS & JS you will now need to purge your Cloudflare cache to see the effect of any minification change.
The Auto Minify option can be found under the 'Speed' Section:
If you encounter any issues with Minification, check out our article that explains why Minification may not be working.