Funny, that’s a complaint I have about Markdown. Anytime I use superscript or subscript, or try to nest markup within a list or table or something, I always get the formatting wrong. Whereas in HTML it’s always easy to nest things properly, even when dropping implicit end tags (which I always do), because the rules are both self‐consistent and standardized across implementations.
I agree nesting is easier with HTML. Most of the content I write is not really nested though, particularly when writing notes, to-do lists, etc. the low ceremony of markdown is a huge win over HTML for simple content.