The manual insert in our case was done by a developer. We (as probably most Hibernate users) do not rely on hbm2ddl to migrate database schema in production, using Liquibase instead. One of the recent migrations involved creating a new entity, corresponding table, and corresponding row in HIBERNATE_SEQUENCES with certain initial value. In some cases this initial value was calculated incorrectly as NULL, triggering the subsequent destruction. It was definitely a developer mistake, but the fact that database schema allows this mistake (as the column is nullable) and that Hibernate reaction is so destructive prompted us to log this issue.
Saying that, I agree it's not that easy to reproduce, so Minor priority is reasonable.