I've never ever had a problem related to covers added via Calibre.
I've used the Calibre Cover Creator, browsed images (my own), the Calibre downloader and used Gimp via Calibre GUI to edit a cover.
The normal way is either to browse or download via the interface in Edit Metadata for a book, or use the Cover Creator plugin from main GUI. CC main use is to quickly add text to a browsed image or cropped downloaded image. It's better to use Gimp and have layers, save as XCF and export a suitable size JPEG. Then text can be edited or image changed without changing text.
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