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The page numbers are still hidden in your pdf, even though you've cropped them. Most pdf cropping tools just change the page borders, all the text stays the same. Even if you use Adobe Acrobat to crop it you still need to go into some buried pdf optimization options and tell it to discard hidden text.
The only way to fix it in Calibre is to use the remove header/footer regex functions. Click the magic wand next to it to try and create the removal pattern.
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