It's not clear to me what your current situation is, but the root cause of the problem is that the table MSreplication_subscriptions is missing somewhere, possibly in the database HUBCMSSYS1. Assuming that this database is a subscriber, that table should be there. So I think you need to try to repair replication in this database.
The missing table itself does not cause the script to fail, but there is some poor error handling, so that the stored procedure exists with an open transaction, and then later the upgrade fails entirely when trying to change the compatibility level inside a transaction.