A new feature has been introduced allowing when filtering on the basis of a tag to also include sub-tags.
This feature has been requested for a long time, thanks to Evernote for introducing it.
However, at least in Evernote 10.32.4 on Windows, but I have every reason to believe that the problem is not specific to this version:
The choice between "include subtags" and "exclude subtags" seems to produce the opposite effect of what is expected.
More precisely, I could see that when filtering on the basis of two tags, including the sub-tags makes the notes disappear.