bootstrap.jsin your JS external libs. Since you are using V3, add this link:
https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js-- no tool would have found that, most likely. You just have to find that info in the docs.
@MojammelW - the way that I usually use it for CodePen projects is to run the project in the debug view, right click, and "View Page Source". Copy and paste that into the validator.w3.org "Validate by Direct Input" tab, then run the "Check" - it will dump a bunch of errors if you have them.
But you don't need it for this navbar problem - just add that JS, and re-run your page, it should work. It did for me.
wellclass doesn't exist in Bootstrap 4, which is the default in codepen. To use Bootstrap 3 (which has the Well class), replace your link to bootstrap in your codepen settings with: https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css