These bottom-linked scripts are redundant, and depending on how they were written, may cause their primary instance to fail.
Any time you add a script to the application.js either literally or with require tree, it gets inlined and minified into the one monolithic application.js file, and linked at the head level of the page. If your script is explicitly written to be linked at the bottom of the page, then it may not be prepared to wait until all the rest of the page is in place before trying to find its referenced elements. This will fail because it is referencing a page element that isn't there (from its point of view at the top of the page). If that error isn't caught properly, then the script can cause later scripts to either fail as well or never even try to run.
Walter