Hello,
JoomSEF only creates SEF URLs for the links that are generated in the HTML source code. It does so when first time detecting the links.This means it will not generate any URL by itself.
So, if the SEF URL to category-list layout is generated, there must exists a link in souce code, that points to it.
Try enabling URL source tracing in advanced configuration of JoomSEF and see, wherefrom the links you do not want get generated. (you will be poited to the source file where from the SEF engine is called)