This known as "Duplicated URLs" issue and happens because there exists 2 links to the content/category in your site - 1 with category list layout and the other with blog layout.
At the start, MijoSEF find the link to category with one layout (mostly blog). So the appropriate URL is created and works fine...
... until another link is detected (mostly generated by 3rd party modules), that leads to the same category, but with different layout setting. Then another records is stored to database and possibly it automatically gets preference over the prior link stored. Check the following link to resolve this issue:
http://www.miwisoft.com/support/docs/mijosef/how-to/how-to-reduce-or-prevent-duplicated-urls
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