I would say, this should be a problem with the structure of the two particular e-books. The lack of chapters, too, suggests this might be the case. I've read quite a few heavily footnoted books in Marvin, and haven't noticed the behaviour you describe.
As a workaround, I would suggest, after you read the footnote, to use Marvin's "Tap for last position" link at the left bottom of the screen to return from the footnotes section to the main text. This should allow you to continue reading the book normally.
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