I think you have selected install option instead of upgrade, if you have chosen right option then it could be defect, if it is dev environment and the previous snapshots databse backup is there then revert the setup and try to upgrade the same and check you face same issue or not. if you have taken screenshots or upgrade logfile is with you then please share the same.
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you may have installed instead of upgraded or the installer didn't cleanup the older version on upgrade. you can just delete the old links if they are actually old links.