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IMCE is recording each file uploaded through its interface both in the file_managed table (that's fine) and in the file_usage table. As a consequence, it is impossible, for instance, to subsequently delete a file through the Media user interface, because such file appears to be in use by some entity. For comparison, when a file is uploaded using the Media module (at admin/content/media), the file is registered in file_managed, but not in file_usage.
The documented purpose of file_usage is to “track where a file is used” (see also file_usage_add()). That is, to associate a file to another object (a node, a user, etc…). If the file is not used by another object, it should not be tracked there. As IMCE is not used to attach files to nodes it should never touch the file_usage table.