When viewing a Markdown file and selecting a line in the Table of Contents inspector, the document display jumps to the correct position in the document but aligns it to the bottom of the viewing area instead of the top or center where it is expected.
Assuming that you’re previewing the document and not editing it then this is a limitation of macOS’ WebKit framework, it’s only possible to scroll to certain positions to make them visible but not to specify a certain alignment.