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Do you mean the last line of a page is not always exactly at the same position? That's unavoidably without grid typesetting, which as far as I know is not a feature available for reflowable ebooks. Add the margins and line heights of the chapter header and the last line of the page could be anywhere. Any other page where there is a non-running-text element (a header, an image, a scene break, a text block with different font size, a poetry fragment...) will have the same effect.
If it bothers you a lot, you could try micro-adjusting the font size and line spacing to find the sweet spot where the header height happens to match exactly an integer number of normal text lines. But that will be different for every book (and page).
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