I assume this means:

• Page A has template {{foo}}
• Template {{foo}} is in [[Category:1]]
• [[Category:1]] is removed from {{foo}}

?

Pretty much (not only the template is in category (aka [[Category:1]] is not within <noinclude>)), and vice versa.

Same when the category is added/removed via module.

So issues with noinclude tags I have grouped with T126139

As for what I thought this issue was about (regarding a page being in a category through both use of a template and actually in the page text) I just did a quick test and don't seem to be able to reproduce it.

:@Danny_B Could you give a step by step reproduction?

Change 281195 had a related patch set uploaded (by Addshore):
CatWatch don't show the number of pages transcluded

https://gerrit.wikimedia.org/r/281195

Change 281195 merged by jenkins-bot:
CatWatch don't show the number of pages transcluded

https://gerrit.wikimedia.org/r/281195

@Danny_B do you still find this an issue now that the summaries do not try to refer to all pages that include the page with the category change?