I have two entities, User and Roles each one with active boolean parameter and ManyToMany relationship.
This boolean parame
Users with @OneToMany relationship to Roles. User-1 : Active-Role-1, Active-Role-2, In-Active-Role-3
User-2 : In-Active-Role-3
User-3 : Active-Role-1, Active-Role-2
User records that satisfy your condition (have at-least one an active role) User-1
User-3
This is where the role of your where conditions end. Once it has been decided which record id to fetch, JPA will fetch those User records in full. User-1 and User-3 with all their associated roles (including inactive). It might do join or another select but whenever it does, it will fetch all of its associated fields
In summary, Once it has decided to fetch an entity, it cannot do any filtering on its associated fields. In this case, you expected a filtered objects in user.getRoles() but it cannot.
If JPA had allowed that, it cannot do dirty checking, cascading or repeatable read. So it does not allow it