I was asked to report this bug after doing the last update.
The error was something about a zip file permission denied, but going back the the page it now looks like there is no error. This is all I copied:
piwik\plugins\CoreUpdater\Updater.php(219): Warning - unlink
Without the exact error it’s hard to tell what went wrong. Can you check if your webserver has write permission on the Piwik folder?
If you wan’t to make sure the update replaced the files correctly check the Integrity Checker (In the system check menu) or do a manual update.
Yes - the server has write permission on the Piwik folder. The auto-update did work. It is just that there was this warning flag with error. Now it is not there any more.