Calling EntityManager.createNativeQuery calls NativeQueryImpl.setZeroBasedParametersIndex, which in turn calls ParameterMetadataImpl.setOrdinalParametersZeroBased(false). ParameterMetadataImpl is shared between threads for all sessions, and so one thread is getting the 'true' version of isZeroBasedParametersIndex(). It probably happens the first time 2 EntityManager objects on different threads try to run the query at the same time.

EntityManager is being used on a single thread. I can't easily reproduce this, except in a specific integration test while playing with setOrdinalParametersZeroBased. It happened in Confluence while deleting a space for a user one time after running in production for all instances in Confluence Cloud for 9 hours.

Positional parameter [0] not set
at org.hibernate.query.internal.QueryParameterBindingsImpl.verifyParametersBound(QueryParameterBindingsImpl.java:255)
at org.hibernate.query.internal.AbstractProducedQuery.beforeQuery(AbstractProducedQuery.java:1307)
at org.hibernate.query.internal.NativeQueryImpl.beforeQuery(NativeQueryImpl.java:222)
at org.hibernate.query.internal.AbstractProducedQuery.list(AbstractProducedQuery.java:1396)