Hello,
this happens because there exists 2 links to the conent in your site - 1 with category list layout and the other with blog layout.
At the start, JoomSEF find the link to category with one layout (mostly blog). So the appropriate URL is created and works fine...
... until another link is detected, that leads to the same category, but with different layout setting. Then another records is stored to DB and possibly it automatically gets preference over the prior link stored.
There is a few ways to solve this:
After the second links is generated you can click "active" in URL Manager to chooe, what layout you want to use for given SEF URL. (in case you want to use just 1 layout always); If you would like to use both, you will need to change one of the SEF links to something else, so the 2 are not conflicting.
You can also prevent such "duplicates" creating by changing JoomSEF configuration. Then only 1 version of SEF URL will be stored - and in case it is not the one you want - you will need to update it manually.
Another option would be to update your site in a way, that there do not exist links with both types of layout. - then no duplicate URL can occur.