Have been using the previous version of Krita 2.8.5 and followed the instructions on the website to install the new version but is it possible to start the application from the desktop and without using the terminal? Not sure if it is important but this message shows up when its started from the terminal,

"krita(11796)/koffice (lib komain) KoPluginLoader::load: Loading plugin "Textdocument Inspection" failed, "Could not find plugin 'Textdocument Inspection' for application 'krita'" "

Also it seems to have made duplicates of all the test brushes that were made in the previous 2.8.5 version, and these are unable to be deleted. Tried going directly to the brushes folder through this directory "/home/[username]/.kde/share/apps/krita" but the brushes folder is empty. Is this a common bug or are we doing something wrong?

Sounds like you didn't completely remove 2.8.5 before installing 2.9. The default brushes are located under '/usr/share/kde4/apps/krita' which is why you're not finding anything in your home folder. The one under the home folder is used to install custom brushes.