This issue came up during beta-testing, but in each successive Beta version, Kris reduced the issue, until apparently all the beta-testers' books were displaying correctly for us, so that it was reasonable to suppose that the issue was completely resolved. There can still be a "rogue" book or two, however, where the issue may unexpectedly rear its ugly head again, although as you say, Kretzer, there is no reason for this to be happening, based on the EPUB's code.
This is, in fact, no Marvin issue, but apparently an iOS (WebKit) bug -- sometimes, it can also be encountered (or intentionally reproduced) in Stanza, iBooks or other iOS e-readers. Only yesterday, I was posting to the Marvin betagroup two screenshots from Stanza on the iPhone, to illustrate the opposite of what you are reporting here: one and the same book (the same EPUB file) displays perfectly fine in Marvin for iPad, but in Stanza for iPhone, the same e-book has bottom lines cut off, both in Day Mode and Night Mode. Enjoy the two Stanza screenshots below.
This is the first time in years I've seen this happening to such a critical degree in Stanza. The book is completely unreadable in Stanza on iPhone, so I had to switch to Apabi Reader for this particular book on the iPhone.
What happens is that the entire screen content is pushed downwards on the screen, resulting in a tall, empty top margin on the screen, and therefore not enough space left at the bottom of the screen for all lines that should be there. Just out of curiosity, Kretzer, have you tried adjusting paragraph spacing for this particular book? If so, does the issue go away, does it get worse, or does your preferred paragraph spacing make no difference?