@thewarbringer123 Using both Asset CleanUp and Autoptimize is fine (many users are having this plugin combination) and there shouldn’t be any problems if they are set up correctly. For instance, if you enable optimize/combine CSS in Autoptimize, don’t enable it as well in Asset CleanUp (this should be prevented automatically by the way), since the server will be using more resources (because of the redundant features) and you could end up with extra disk space that is used when it’s not necessary.
My recommendation would be to use Autoptimize for combine/minify CSS/JS if it gives the outcome that you need and Asset CleanUp for unloading useless CSS/JS (stripping the “fat”), thus the files that will be combined/optimized by Autoptimize will be at the end smaller, take less disk space and the pages will load faster as the browser won’t have to download large files with all the “crap” on them.