Until Kovid comes along..
I don't know if this is the cause, but the immediate question is, with the template:
{author_sort}/{series}/{series_index}{title} - {authors}
What happens if there is no series and hence no series index? You might want to try the following:
{author_sort}/{series}{series_index:0>2s| - | - }{title} - {authors}
I suspect that will solve it, but you will lose the extra folder.
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