One case in which this often happens is when printing PDFs. Some PDFs appear to GreenPrint as though each page is one image, rather than a combination of text and images or whatever the case may be. This could cause pages to be flagged as waste when they are not. If all of the pages in your document are flagged as waste, we suggest using Control + A on your keyboard to select all pages, and then choose Include Pages from the hover.
Another case when GreenPrint could make a mistake is if a page looks entirely blank to you, but it actually contains some hidden images so it does not get flagged as waste. In this case we recommend using the Remove Page option on the hover.
Don't forget that you can also customize the GreenPrint filters by going to Control Panel > Printers & Faxes > GreenPrint > Printing Preferences > Rules (In Vista: Control Panel > Printers > GreenPrint > Printing Preferences).