This is caused by following change:

commit 95d29c99f01882ffcc2259f62b3163f9b0e80c75
Author: Marko Mäkelä <marko.makela@oracle.com>
Date:   Tue Nov 27 11:12:13 2012 +0200

    Bug#15920445 INNODB REPORTS ER_DUP_KEY BEFORE CREATE UNIQUE INDEX COMPLETED

    There is a phase during online secondary index creation where the index has
    been internally completed inside InnoDB, but does not 'officially' exist yet.
    We used to report ER_DUP_KEY in these situations, like this:

    ERROR 23000: Can't write; duplicate key in table 't1'

    What we should do is to let the 'offending' operation complete, but report an
    error to the
    ALTER TABLE t1 ADD UNIQUE KEY (c2):

    ERROR HY000: Index c2 is corrupted
    (This misleading error message should be fixed separately:
    Bug#15920713 CREATE UNIQUE INDEX REPORTS ER_INDEX_CORRUPT INSTEAD OF DUPLICATE)

    row_ins_sec_index_entry_low(): flag the index corrupted instead of
    reporting a duplicate, in case the index has not been published yet.

    rb:1614 approved by Jimmy Yang

Problem is that after we have found duplicate key on primary key
we continue to get necessary gap locks in secondary indexes to
block concurrent transactions from inserting the searched records.
However, search from unique index used in foreign key constraint
could return DB_NO_REFERENCED_ROW if INSERT .. ON DUPLICATE KEY UPDATE
does not contain value for foreign key column. In this case
we should return the original DB_DUPLICATE_KEY error instead
of DB_NO_REFERENCED_ROW.

Consider as a example following:

create table child(a int not null primary key,
b int not null,
c int,
unique key (b),
foreign key (b) references
parent (id)) engine=innodb;

insert into child values (1,1,2);

insert into child(a) values (1) on duplicate key update c = 3;

Now primary key value 1 naturally causes duplicate key error that will be
stored on node->duplicate. If there was no duplicate key error, we should
return the actual no referenced row error. As value for column b used in
both unique key and foreign key is not provided, server uses 0 as a
search value. This is naturally, not found leading to DB_NO_REFERENCED_ROW.
But, we should update the row with primay key value 1 anyway as
requested by on duplicate key update clause.