Steps to reproduce the issue

Create a simple simple system plugin. Let's call it aa, because we need to make it first in alphabetical order when we update extensions. The plugin files are the following:

aa.php

defined('_JEXEC')` or die('Restricted access');

class PlgSystemAa extends JPlugin
{	
}

aa.xml

<?xml version="1.0" encoding="UTF-8"?> 
<extension type="plugin" version="3.4" group="system" method="upgrade">
	<name>plg_system_aa</name>
	<version>1.0</version>
	<creationDate>2016-05-04</creationDate>
	<license>http://www.gnu.org/licenses/gpl-2.0.html</license>
	<scriptfile>installer.php</scriptfile>
	<files>
		<filename plugin="aa">aa.php</filename>
		<filename plugin="aa">index.html</filename>
	</files>
	<updateservers>
		<server type="extension" priority="1" name="Aa update server">http://addondev.com/share/test/aa.xml</server>
	</updateservers>
</extension>

installer.php

defined('_JEXEC') or die('Restricted access');

class PlgSystemAaInstallerScript
{
	protected $_counter = 0;
	
	public function preflight($type, $parent)
	{
		$this->_counter++;
		JFactory::getApplication()->enqueueMessage('Preflight called: ' . $this->_counter . ' time(s).');
	}
	
	public function postflight($type, $parent)
	{
		JFactory::getApplication()->enqueueMessage('Postflight called: ' . $this->_counter . ' time(s).');
	}
	
}

You can download this plugin from my website. Then we need to download any localization, let it be English (USA) translation and change the version in xml-manifest to the previous one:

<?xml version="1.0" encoding="UTF-8" ?>
<extension type="package" version="3.5" method="upgrade">
	<name>English en-US Language Pack</name>
	<packagename>en-US</packagename>
	<!-- <version>3.5.0.1</version> -->
	<version>3.5.0.0</version>

After installing the plugin and the language distributive, go to the Joomla Extension Manager, update tab. Update the extensions, see the result. I have made a video that shows the problem

Expected result

Installer methods are called once.

Actual result

Installer methods are called multiple times.

System information (as much as possible)

You can see on the video that the problem arises when the system plugin goes before the localization in the update order. When the plugin goes after the language distributive, the installer methods are called only once, as it is expected.