Hey Dimitris,
the top-left element gets replicated on scroll because it is a sticky element, and probably your setting for the maximum number of portfolio items per page (“Portfolio items per page” option on the “Portfolio Page” tab of the Theme Options panel) is higher or equal to the total number of portfolio items that exist on the website. Please try setting this limit to a smaller number, the additional items loaded with scroll should still contain the sticky one each time, yet it will look much nicer :) As noted on page 12 of the theme manual, the infinite scroll is still an experimental feature which was added only in version 2.0 following several requests from the users; that same part of the manual lists the current particularities and limitations of the Infinite Scroll feature.
Regarding your second question: the pages containing portfolio items that have a particular tag are generated automatically within the theme, based on the “taxonomy-tagportfolio.php” template file; their URLs are of the form: http://www.example.com/tag-portfolio/%5Btag-name%5D. Here’s the example from the demo: https://satoristudio.net/ikebana/tag-portfolio/services/. If you need to include such a page into the top menu, you can use such URLs and add custom menu items with direct links to tag archives.