So this happened a lot in previous versions of Illustrator and I could trash my extensions and fix everything. Problem: when I place images, it will automatically embed placed images, making my file sizes huge. Seems to do it more with PSD files, wanting to flatten, etc. How do you reset the extensions in 2014?
This issue is more about Illustrator than Extension Manager. I am afraid it's better to post you question to Illustrator. If you are sure the problem was caused by a specific extension, you can disable or remove it in Extension Manager.