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When using the highlight shortcode for code blocks in lists, the indentation needed to have the code blocks indented gets added to the code block itself.
This does not happen when using code fences.
So the bug seems to be localized to Hugo and not Blackfriday.
In the same test page above, the first section has the same code blocks, but done using the code fences, where that extra indentation issue is not seen.
Another effect of not removing that indentation is that the indentation before the closing {{< /highlight >}} creates an extra blank line in the final HTML.