Sequence issues can be caused by the environment being refreshed from another environment using a "hot" backup (while Clarity services are still running).
It's recommended to take the backup when there is minimal activity in the environment if possible.
See 11285 for steps on how to fix sequencing issues.
Once sequencing issues have been fixed, retry the upgrade.
On Premise customers: One other option is to restore the environment from prior to upgrade, the take a "Cold" backup of the source environment (where Clarity PPM Services are down).