eladmarmor Hi. All articles are showing on a category page if there are no separate menu links made to this article. Masthead is a module, You just need to disable it from showing on that category/article (whatever was used), it will use article title and date/author informations instead (like on other articles).
For not working links I can see the url for PREV is same as the article shown currently. I'm afraid joomla's pagination has some problems recently. But to be 100% sure it's not caused by template please rename /html/pagination.php to /html/0pagination.php in template's folder.