This is a well known problem, which is well described as a bug in Zend Framework’s issue tracker. Once you add some scripts with the inlineScript helper you’ll receive them twice in the code. This makes the page slower and leads to some crashes.

$scripts->appendFile('my-file1.js')
        ->appendFile('my-file2.js')
        ->appendScript('alert("test")');

This will print the alert twice.

Quick Solution

Although this is the worst solution I’ve ever made – it works! There is a check for duplicates in the HeadScript helper around line 240:

if (!$this->_isDuplicate($content)) {
...

and then a check in the _isDuplicate method(), ~ line 270:

if (($item->source === null)
    && array_key_exists('src', $item->attributes)
    && ($file == $item->attributes['src']))
{
    return true;
}

The thing you’ve to do is to add such a check for the appendScript() and not only for appendFile() method – again ~ line 230:

case 'script':
	if (!$this->_isDuplicate($content)) {
	    $item = $this->createData($type, $attrs, $content);
	    if ('offsetSet' == $action) {
	        $this->offsetSet($index, $item);
	    } else {
	        $this->$action($item);
	    }
	}
	break;

And then slightly modify the _isDuplicate method:

foreach ($this->getContainer() as $item) {
    if (($item->source === null)
        && array_key_exists('src', $item->attributes)
        && ($file == $item->attributes['src']))
    {
        return true;
    }
    if ($item->source == $file) {
        return true;
    }
}
return false;