This does happen sometimes, even when the pages are measured out to the right size. And I'm afraid I haven't been able to find whether it's a bug that I could easily fix, or if it's just a limitation of how Zine Arranger currently does the layouts. I'm suspecting the latter.
Whenever I do another big update, I plan to look into a using whole different approach which should let it get more precise, but that's going to require quite an overhaul. For now it's just probably going to end up a little wonky sometimes, though hopefully it won't be too terribly noticeable once the zine is folded.