CatWatch does not reflect (un)categorizaction via transcluded templates when such template is changed.
|mediawiki/core : master||CatWatch don't show the number of pages transcluded|
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?