Driver support for (older) graphics cards.
The screen tearing issue (may be related to above)
Dependency hell.
How a program or game used to work fine on an older version but doesn't work anymore. Basically lack of backwards compatibility for software.
How you can't always do everything you want in the gui and have to use the terminal sometimes and know some of the basic commands.
How a lot of the gui programs don't have (usefull) error messages so it just leaves you confused when a program you installed doesn't want to run.