It usually doesn't matter how you are pinning to Start11 (or Start10 or Start8) if you use the following procedure. When I pin something to Start11 (Windows10), it is from an app or shortcut that gives the option to pin to Start11. Remember, this only started after the last update (1.24). Prior to that, I never had a problem with pinning to Start11 or any of the other Start Menus. Pinning an app or shortcut to Start11 worked fine until the update. Icons always were placed below all the other icons. In 11, it forces them into the icons on top and messes up the menu.
I'd just be happy to revert back to the previous version but that doesn't seem possible.