The modern debugging template also loads jQuery, which breaks any pages which use jquery and plugins.
Any jquery plugins used by the page are loaded into the first jquery instance, then the debugging template loads a second jquery instance which doesn't have the plugins and any use of the plugins then throws an exception.
jQuery has a no conflict option to avoid this problem.
attached is a simple demo script, if you run it with out debugging enabled it runs fine.
if you run it with the modern debugging template enabled, you will see the following error in the console