I don't know if this is intended behaviour or not, but I just spent some time debugging this.

If you execute a native query using hibernate, and the resulting column names are identical, all your columns will have the same result.

Take the following example query.

select * from
( select count(distinct tr.id) from <…> where <…>) as t0 join
( select count(distinct tr.id) from <…> where <…>) as t1 join
( select count(distinct tr.id) from <…> where <…>) as t2 join
( select count(distinct tr.id) from <…> where <…>) as t3

MySQL yields

count(distinct tr.id) count(distinct tr.id) count(distinct tr.id) count(distinct tr.id)
122 111 239 208

Hibernate result yields an Object[] = {122,122,122,122};

select * from
( select count(distinct tr.id) as col0 from <…> where <…>) as t0 join
( select count(distinct tr.id) as col1 from <…> where <…>) as t1 join
( select count(distinct tr.id) as col2 from <…> where <…>) as t2 join
( select count(distinct tr.id) as col3 from <…> where <…>) as t3

MySQL yields

col0 col1 col2 col3
122 111 239 208

And Hibernate yields the correct result Object[] = {122,111,239,208}