Cloudflare's Rocket Loader is a superior way of optimizing JS delivery. While it works flawlessly on 9 out of 10 sites and can give your site a dramatic speed boost by drastically reducing the number of HTTP requests, sometimes you may need to exclude some scripts to make it work without breaking your site.
To give credit where credit is due, I've included several articles addressing the commonly known issues and how to fix them.
Please keep in mind that you should only use one method for optimizing JS at a time. If you're using Rocket Loader, then don't use Autoptimize or another plugin for the same purpose and vice versa until you made sure this works without breaking the JS.
Also, when you're working on JS it's best to keep Minify JS (under Speed on Cloudflare) unchecked if you're using another tool for JS minification. Using several tools for the same task often leads to broken JS.
Here's some articles to help you fix JS errors when using Rocket Loader: