Bugs

html/epub: numbering is limited to first level
epub: no way to embed custom files to epub
no support for footnotes and tables (but I don't even know how to make them in Markdown)
latex: no support for links and images
latex: characters are not escaped for LaTeX, which sometimes causes issues, particularly when there is code/formula
config: can't handle multiline string (and really, isn't there an existing format for that?)
config: can't parse specified numbers for negative chapter (is it really a bug?)