Reproduction steps:
The link should point to https://commons.wikimedia.beta.wmflabs.org/wiki/Special:UploadWizard but instead sends you to https://commons.wikimedia.beta.wmflabs.org/wiki/Commons:Upload . On production this problem doesn't appear to exist.
With JS or no JS, the link points to https://commons.wikimedia.beta.wmflabs.org/wiki/Special:Upload for me. Also note, that's where it suppose to point not Special:UploadWizard
What does your HTML look like? I see this:
<li id="n-uploadbtn"><a href="/wiki/Commons:Upload">Upload file</a></li>
This is what I see.
</a></li><li id="t-upload"><a href="/wiki/Special:Upload" title="Upload files [u]" accesskey="u">Upload file</a>
But... I am seeing yours too.
Actually there are two upload links; there's one in "Participate" section and there's another in "Tools" section. The one in the latter section is what I saw first and it has correct link and html. The one you saw is in the former section.
The canonical link added by Skin is in the Tools section. The incorrect one that you saw was added manually to the sidebar in this 2011 edit. The url definition is at https://commons.wikimedia.beta.wmflabs.org/wiki/MediaWiki:Upload-url.