Known Issues
The following issues are known, however unrelated to AutoLinks and are related to Joomla! or some other component:
SEF URL by AutoLinks is incorrect
AutoLinks may generate a incorrect or partly incorrect Link with Joomla! SEF enabled. This is caused when a Article ID is equal to the Category ID the Article is published in. That is a error of the Content Router Component of Joomla and is correctable by modification of the following Joomla! Core File:
components/com_content/router.php
/* Line 70: */ if (isset($menuItem->query['id'])) { /* change to: */ if (isset($menuItem->query['id']) && $view==$mView) {