When the Wiktionaries went case-sensitive, the file usage checking from Commons became case-sensitive. However, the case-sensitivity on Wiktionaries applies only internally, and does not apply when an external link is made to another project. In particular, links from a Wiktionary to files on Commons are not case-sensitive because the link is made to a case-insensitive project.
As a result, Commons file usage information only displays some of the instances of a file used on the Wiktionaries. For example, File:La-cls-discipulus.ogg is used on the English Wiktionary, but its page on Commons says "There are no pages that link to this file."
Commons should realize that links made to it from *any* project are de facto case-insensitive because it is itself case-insensitive.