When you insert a single line break in the editor, it creates a single line break within the current paragraph. Two new lines are required for a new paragraph, which is why the last line in these examples ends up bundled with the quote. Pretty sure this is by design in Markdown.
However, I think I can mitigate it by inserting an empty bracket at the end of the quoted post in the reply form. That way, even if this happens…
> Quoted text. > Reply here.…it’ll work.
That will probably help mitigate it. Not sure how much time you need to spend on something that sounds like markdown’s issue.