In the document I linked above, it lists the hard-coded folder names which are excluded from scanning; one of them is “Sub-folders that include the words extras, samples, …” I suspect that, since your folder structure has additional levels of organization between the root of your library and the movie, you are being affected by this rule. It seems that it really looks for “extra” and not “extras” however.
And, for what it’s worth, the new Plex Movie agent introduced in Plex Media Server versions 1.20.x.x and later do not seem to have the same “problem.” That is, the additional, nested folder level doesn’t cause the movie to not be scanned.
