This is a common problem when using multiple JavaScript libraries as many of them define $()
SharePoint is using ASP.NET Ajax so if you include JQuery you should do that in noConflict mode.
You turn that on using
jQuery.noConflict();
Now $ will never mean jQuery unless you use constructs like:
jQuery(document).ready(function($){
/* code using $ */
});
or
(function($) {
/* code using $ */
})(jQuery);