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I have this same problem. All of my ebooks are mobi or AZW3 format. And half of my covers are incorrect. Mostly they are for some other book in the same author's folder. But sometimes they are some other image from within the book. 

I'm sharing a Calibre library in Ubooquity. Calibre library puts the cover in a 'cover.jpg' file in the same folder. So perhaps when settings option 'Shared books are in a Calibre library' is checked, Ubooquity doesn't need to guess at all. I just needs to pick the cover.jpg file in the same folder as ebook file. Please implemented a fix if possible.

BTW, for reference, I have Ubooquity 2.1.2 installed on a QNAP NAS.