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You have restored a Joomla! 5 site on top of a Joomla! 3 site without removing its files and folders. However, this is what we tell you in our documentation:

Do not try to overwrite one Joomla! version family with a different one. Overwriting a major version with another (e.g. restoring a backup taken on Joomla! 3.7 on top of a site running Joomla! 2.5 or vice versa) or between different minor versions (e.g. restoring a backup taken on Joomla! 3.7 on top of a site running Joomla! 3.6 or vice versa) will NOT work. Joomla! moves files around between minor and major versions. Since the backup does not delete files not present in the backup archive this will end up with Joomla! being "confused" and malfunctioning. In these cases you should delete the existing files and folders (except, perhaps, user generated content) before restoring the backup. You can safely restore a sub-minor (path-level) version on top of another. For example, you can safely restore a Joomla! 3.7.5 site on top of a Joomla! 3.7.3 site or vice versa.

https://www.akeeba.com/documentation/akeeba-backup-joomla/restoring-backups.html#general-guidelines

Kindly note that Kickstart does have an option to delete all existing files and folders before restoring a backup. It's disabled by default as it's a quite drastic and potentially dangerous operation, therefore requires explicit user consent to carry out.