css stands for Cascading Style Sheets which means all files in the same directgory with the .css extension will be loaded and if more than one stylesheet contains the same directive, the last one loaded will be the one used. This is NOT something peculiar to Zen Cart. It's the way stylesheets work. If you are coding your own stylesheets and html, you can control the order. If you're dynamically building pages (like ZC is), they're loaded in order based on the names (alphabetical, numerical). Bottom line is, if you're not using the stylesheet, either delete it or give it an extension other than .css

Check out http://www.w3schools.com/ for some good information about stylesheets, html and tons of other subjects.