Well, there is good reason to duplicate internal links at the bottom of a page, for instance, to help user navigation, without the need to scroll to the top of the page. Especially if the page is quite long.
In fact, I would consider it good practice, in that situation.
If SEs has an issue with that, so what, I have a higher regard for my visitors experience than I have for any (supposed)SE centric tweaks.
And a good experience may well increase payed clicks, too, if that is an issue, who knows.;)