I believe this is a feature request rather than a bug report.
Typora is a WYSIWYG editor, which our current editor is not (WYSIWYG is on the long term roadmap). If you check Typora’s source code mode (accessible in the </> button at the bottom), the numbers aren’t aligned either.
There’s custom CSS that can help you achieve this, by reserving the certain amount of space, but it might not be the solution for everyone. For example, if you want to reserve enough space so that even the 1,000th item looks aligned, that would leave too much empty space for the first few items.