Table layouts were often broken, with text overlapping into adjacent fields. Unicode font fallback didn't work properly, with characters like "→" being silently dropped because they didn't exist in the main font. Having predictable control of page breaks, to avoid situations where header text didn't stick to the following paragraph and instead had header and paragraph text split over a page boundary, was pretty much impossible.
I ended up concluding that Markdown isn't a sufficiently powerful markup language for page-based documents, and went back to using Word in all its WYSIWYG delight.
That said, maybe there were ways of doing all of the above but I couldn't figure it out and found the whole process of wrestling with with both Markdown and LaTeX templates, and Pandoc configuration, unintuitive and annoying.