There is a propensity for Joomsef to unnecessarily add -2.html, -3.html, etc. to many of my pages and articles. e.g. I don't have any links to a given category on the menu, only to a single blog section. But Joomsef will create links to each category, even though they aren't linked in a menu... /category-page-2.html, etc.

Joomsef will also perform likewise with AlphaContent. It will take a section and then add -2 , -3 to each article within a category. e.g. first category: /sectionorcategory/this-page-is-hosed-2.html, or /sectionorcategory2/this-page-is-hosed-3.html.

Is there a way to avoid this?

Have you checked the JoomSEF FAQs - I am experiencing duplicate URLs like -2, -3, etc. What should I do? on this topic?

Well I still can't figure this out.

in global config I have disabled Ignore multiple sources,
and for alphacontent plugin I have enabled Ignore multiple sources

cleared cache and recreated sef, but still I get multiple sources created in alphacontent.

How can you solve this and have correct and preserve itemid of article and not duplicated that don't use the correct itemid?