I found this bug a few days ago. If you edit any published post and then save it, the sitemap changes all the urls' permalink and the category is removed from permalink. Here's an example of what I'm trying to say.
The sitemap first displays urls like this: http://www.example.com/this-is-a-category/this-is-a-post
After editing any published post and clicking save, the sitemap changes all the urls and displays urls in this format:
The sitemap displays post permalink with double slash and the category removed. After rebuilding the plugin manually or publishing a new post, it resumes back to normal.
This is really bugging me a lot and is affecting my SEO. :(