If the cover is not properly marked (semantics for both the file and the image used), it is a guess. OTOH PDF uses just uses the first page.
If you use the ebook editor (T),
right click the image:use as cover
Do the same for the HTML file that uses that image:
Now, when you go to the Metadata Editor screen. Select the EPUB format and click the blue-blank cover button to the left, and that will bring that currently marked cover into the Library.
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