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That is, probably, working as designed.
From the description, I guess you are sideloading epubs. For these, Kobo create the cover by rendering the first page of the book. So, if the first page has a small image stuck in the top left corner, that is what the device will show. You should see this when you open the book on the device, the calibre viewer, or any other epub reader. If this isn't the case, I'd need to see an example to see what was going on.
The, to me, best fix is to fix the cover page in the book. Calibre can do this with a conversion or the Polish books function. Or you can edit the books.
You can also have calibre generate the cover images and send them to the device when sending the books to the device. There is an option in the driver to do this. And for books already on the device, you can use my Kobo Utilities plugin to send just the covers.
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