See http://en.wikipedia.org/w/index.php?title=Special:WhatLinksHere/Template:Paleo-amphibian-stub&hidetrans=1. Bug seems not to happen all the time - for example, http://en.wikipedia.org/w/index.php?title=Special%3AWhatLinksHere&hidetrans=1&target=Template%3AUncat&namespace=0 (Template:Uncat limited to article namespace) shows no results, although there are 5 transclusions).
Version: 1.16.x
Severity: normal
This can happen if the template contains a link or #ifexist call referring to itself. In this case, the template appears to have a "v" link which does exactly that. So pagelinks entries get added from all pages which include the template.
There may be a bug open for the underlying issue, which is that pagelinks is primarily for cache invalidation, and is often wrong when used for "what links here". Links inside templates need to be registered so that all the including pages have their caches invalidated when the linked page is deleted.