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It may. It's an opcache issue. While we try to use opcache_invalidate() on the file that was triggering the error there is absolutely no guarantee that this will work. It depends on the PHP configuration, whether PHP actually invalidates the file and whether another plugin has already loaded the file that is causing the problem (administrator/components/com_akeeba/Container.php).

Doing the double install in a row WILL work in most cases because:

• if it's an opcache issue our post-installation code runs opcache_reset() which invalidates the entire opcode cache (PHP opcache) starting with the next request, i.e. the one after the failed installation.
• if it's a plugin our pre-installlation code has cut its balls deleted its files which means that in the next installation attempt it will NOT be loading.

This would all be prevented, of course, if Joomla was a decent CMS. I had written a white paper circa 2012 about how to improve the extensions installer. Part of that was running the pre-installation, installation and post-installation in separate page loads to avoid this exact kind of issues. The pre-installation code would be disabling the plugins being updated and clearing the opcache (for the next page load, i.e. the installation / update), the installation / update code would run in a new page load without these plugins interfering and with opcache reset (and reset it again since it has just installed a bunch of new .php files), the post-installation would also run clean and re-enable the previously disabled plugins. This also had a provision for a roll-back in case any part of the installation process fails. Of course the "enlightened" leaders don't really understand any of that and this proposal went exactly nowhere.

All I can do now is have my pre-installation code try to do as much as it can but it CAN NOT unload PHP classes; PHP doesn't support that. So if it comes down to having to replace a class already in use you will get an error and you will have to run the update once again.