Sigil routes files into the correct folder according to the file's extension. Thus, JPG's, PNG's, SVG's etc. end up in Images; HTML, HTM, XHTML end up in Text etc.
Anything Sigil can't figure out ends up in Misc.
But if you added a file and it ended up in Misc, it should still be there after saving and then loading the file. If it's not, create a new issue on the tracker.