When logo inserted, empty link appears in menu

On my website I have the latest version of Thorium installed. Today I inserted a logo of the site using the WP standard customizer. After that, there is now an empty box above the “homepage” menu item. It won’t go away unless I remove the logo from the site again. The menu items are also not aligned any more. I have tried finding CSS and PHP related to the menus and header, but without success. Has anybody experienced the same or similar behaviour?