If you’re having problem with mootools.js here is the fix.

Put the code below in your custom joomla template:

$headerstuff = $this->getHeadData();
$headerstuff['scripts'] = array();
$this->setHeadData($headerstuff);
?>

See the image below:

The code above will remove all the prebuilt javascript in your joomla front end page.

To remove a specific javascript use this one:

$search = array(‘mootools’, ‘caption.js’);
// remove the js files
foreach($this->_scripts as $key => $script) {
foreach($search as $findme) {
if(stristr($key, $findme) !== false) {
unset($this->_scripts[$key]);
}
}
}

The code above will remove the mootools and caption.js in your joomla front end page.

Click the link below to read the whole discussion:
removing mootools from the header (joomla1.5)