Hi there,
1. This script is required for menu and is loaded by default:
generatepress/assets/js/menu.min.js
You also have the Navigation search which uses this script:
Navigation Search: generatepress/assets/js/navigation-search.min.js
2. Links in the post, aside from the Smooth Scroll option in GP, which you don’t have enabled by the looks of it, there is no scripts in GP that interfere with those. If that issue persists, then its more likely a plugin such as ToC or an analytics script that is scraping links.