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This is caused by the settings in the epub, which can use <em> measurements for the margins--that is, the margins are a set number of "em-widths," based on font size, instead of a set number of pixels.
It's common to do this with indents, so that as you expand the text, you don't have tiny indents that you can't see at the new size. It's unfortunately also common to use as margins.
The way around it is to edit or reconvert the epubs. (If it's a DRM'd epub, there's no simple way to fix it; the file would have to have the DRM stripped before it could be edited/converted.)
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