In a 286 page guide, publishing to Printed Documentation (PDF), noticed that the output went from 286 pages to 383 pages. The last 97 pages were duplicates of pages within the 286 original pages.
Tracked down the cause: in Printed Documentation>Content there is a checkbox for "Include all referenced topics." Uncheck it, and the PDF output returns to 286 pages, the correct number, and no duplicates at the end.
Since this guide project has several cross references to other topics within the publication, I suspect that if the checkbox were checked (which may be its default), these duplicate 97 pages are added at the end of the PDF. Maybe to assure that cross-referenced topics are included in the output, although, in this case, all of them were already appearing in the first 286 pages?
A complex project, with output to PDF and online/HTML5, with separate TOC's for printed and online/HTML5, plus the latter using condition tags to exclude topics from a preview version that appear in a full version, my speculation is that this may be needed to link to cross-referenced topics otherwise condition-tag-excluded by placing these at the end of the PDF?
Wanted to share this so others who encounter duplicate pages at the end of a published PDF can find this solution, if useful.
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