A big issue that can arise when making a site with many extensions is JavaScript conflicts. If your having an issue with a feature or extension not loading in the template such as menu dropdowns, galleries, etc; this could be due to a JavaScript conflict.
There is no simple solution other than finding out what JavaScript is loading and turning them off one by one until you find the conflict. One way to find JavaScript issues is to install an inspector like Firebug to find the conflict.
The best way to find what JavaScript is loading is to use the View Page Source option in your browser and look at the
area and look for for the .js files the site is loading