Lack of documentation: even comments in the code would be enough, but often there are not even that and to understand what a piece of code does, one must hope that at least the variables are sensibly named;
Libraries not updated because "It's just work in this way..."
Lack of configuration files: important variables, constant, url, server port, etc, inside the code (like spaghetti style) and not in a custom file to import or use.