There is an issue with the way that the Incoming links and Outgoing links lists are populated for each page, currently it is picking up all links which uses the standard [alias|link] and [link] syntaxes, however, it does not pick up those that uses [alias|link|tooltip].

To replicate, simply add a link to a specific page to any other page which uses the [alias|link|tooltip] format, then view the Outgoing links list for the current page, it will not get picked up, if you try it without the tooltip, it is picked up normally.

Regards,
Bo Wang