This looks like an issue with a gadget?

If this is https://ja.wikipedia.org/wiki/MediaWiki:Gadget-ReportIssues.js there's some problems with that code.

It doesn't look like it works as expected in Minerva and L21 should be

pos = document.getElementById( 'p-associated-pages' ) ? 'p-associated-pages' : 'p-namespaces';

rather than

pos = 'p-namespaces';

@Jdlrobson
That script isn't quite a gadget actually. It's just an experimental script made only for demo purposes for a discussion in village pump.
The following code replicates the misalignment issue, so I believe this is an issue of the vector-2022 skin.

mw.loader.using('mediawiki.util', function() {
    mw.util.addPortletLink('p-namespaces', '#', 'MISALIGNED');
});

This is triggering a warning message: "Please update call to mw.util.addPortletLink with ID p-namespaces. Use p-associatedPages instead." indicating the issue here (There does appear to be a typo in this message however)

You can fix this by changing the code to:

mw.util.addPortletLink('p-associated-pages', '#', 'MISALIGNED');

We could perhaps update that code, but in future it will stop working and break altogether so it's probably a good thing that it brought you to Phabricator.

Weird. When I tried to identify the cause of the issue illustrated by the first picture in Op, I didn't see any error message in console but now I get one for the deprecated p-namespaces, and also it's now impossible to reproduce the misaligned portlet link as in the image and in fact no portlet link is added to the position if I use p-namespaces (although this behaviour is normal because it just means p-namespaces is missing. Maybe there was p-namespaces when I initially filed this task but now there isn't? I don't know.) This task can be closed now, it would be a waste of time to try to "fix a bug" for the deprecated feature. I appreciate your help.