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I'm not sure if this is the exact same thing but I'm running into the ambiguous column problem with oracle as well. In my case I've reduced it down to a simple class with two many-to-many sets triggering the issue (testcase attached as hibernate_ora_bug.tar.gz).
I spent some time stepping through the selectString method in org.hibernate.loader.JoinWalker and it looks like the duplicate identifier column aliases are being generated when an inner join is followed by an outer join. I'll look into a bit more tomorrow but I hope someone can confirm my testcase in the meantime.
Environment:
latest hibernate-core-4.2.0-SNAPSHOT.jar (d41545e13b3abe7b)
Oracle XE 11g 32 bit windows
tomcat 7