We experienced this behavior lately. This will appear intermittently for some user in some browser session, try clearing the cache - this will go away.
Is this happening for particular user ? particular browser ? Try to login with the same user in different machine .
You can try to see F12 selector , and compare the CSS .
That's right, because the old one has been deprecated. Hence, the workaround.
If this helps you, please mark my answer as verified.
This is a common issue with upgrades to version 9.0
You can easily remove it from the SiteMap using the XrmToolBox ( https://www.xrmtoolbox.com/ )
See this topic about the same issue:
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