I have upgraded from 3.0 to 3.3.2 and also migrated the site while at it. At first glance everything seems to be working fine, however, there are some issues I can't figure out.
Most importantly, I cannot use user filtering within Admin > Users > Accounts > Browse list of users and Admin > Users > Accounts > Bulk user actions. When I press the "Add filter" button, I am redirected to a bad url, namely one that has an extra "/moodle" in it before "/admin", so instead of "https://mysite.com/admin/user.php" I get "https://mysite.com/moodle/admin/user.php", and an error message reading "The requested URL /moodle/moodle/admin/user.php was not found on this server.". I do not know what the problem is, since I did use the search and replace tool as suggested in the Migration howto. I have grepped mysite.com/moodle in a dump of my database, without success.
The other glitch is with a plugin I installed after the upgrade (Inactive User Cleanup), which is supposed to be available after install from Admin > Reports > Inactive User Cleanup but didn't show up. I installed the same version of the plugin on a different 3.3.2 moodle site, and it worked fine there, so the plugin is not at fault. When I try to reach the page by directly typing in the url https://mysite.com/admin/tool/inactive_user_cleanup/index.php , I get a section error .
It seems to me likely that something has gone wrong during the search & replace , but I don't know how to figure out what. Any pointer would be appreciated.