In the Calibre settings, did you specify the exact version of the Kindle you have as the output device? With that set correctly, and not just left as the defaul

In the Calibre settings, did you specify the exact version of the Kindle you have as the output device? With that set correctly, and not just left as the default, it has been years now since I had any formatting issues going from epub > mobi/azw to read books on my Kindle Paperwhite.