You can adjust the vertical position of the note using the optional argument. This is covered on pages 21-22 of
sample-book.pdf, part of the documentation for the class.
If you have a lot of marginal material which would need manual adjustment, you have a couple of options. First, you can do it manually if you do so after the document content is finalised. Don't do it earlier because changes to the document content will alter what is required.
However, it might be better to look for more automated support. Although Tufte does not offer this, other classes do. Here is the same example using
memoir and without the need for manual adjustment:
Memoir offers extensive support for marginal material of various kinds, including side bars which run to multiple pages, floating and non-floating marginal material and support for marginal 'foot'notes.
KOMA might also be useful but, unfortunately, the English documentation does not include this topic so I cannot tell one way or another.