The most common problem are JavaScript conflicts, you can debug this by making sure you are using no conflict wrappers. Another thing you can adjust is the load order, sometimes there are errors when one script is loader before/after another. If you are relying on many 3rd party scripts it can be difficult, you might have to completely re-do some functionality.
Also check to see if there are any CSS selectors clashing, make sure all the CSS the JavaScript references is unique and separate. Google chrome’s inspect element is a great tool to debug and step through JavaScript.
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