This situation occurs when you use Hibernate as persistence engine and your entities have version field.
Normally the ID field is what we need for merging a detached object with its persistent state in the database, but Hibernate takes the version field in account and if you don't set it (it is null) Hibernate discards the value of ID field and creates a new object with new ID.
To know if you are affected by this strange feature of Hibernate, set a value in the version field, if an Exception is thrown you got it. In that case the best way to solve it is the data to parse contain the right value of version. Another ways are to disable version checking (see Hibernate ref guide to know about it) or load persistent state before merging.