That's correct. Here's what substitutionlist_pkey looks like in the new cluster. From this, it looks like it's actually correct (the oid for substitutionlist_pkey is correct) but pg_upgrade thinks it's wrong and dies. I'll look for the logs you requested and send them separately
db=# SELECT relname, relfilenode, relkind from pg_class where oid = 299749;
relname | relfilenode | relkind
----------------+-------------+---------
pg_toast_17304 | 299749 | t
(1 row)
db=# select oid, relname, relfilenode, pg_relation_filepath(oid), relkind from pg_class where relname='substitutionlist_pkey';
oid | relname | relfilenode | pg_relation_filepath | relkind
---------+-----------------------+-------------+----------------------+---------
2938685 | substitutionlist_pkey | 2938685 | base/16488/2938685 | i
(1 row)
db=# select version();
version
--------------------------------------------------------------------------------------------------------
------
PostgreSQL 9.2.4 on x86_64-unknown-linux-gnu, compiled by gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-3), 6
4-bit
(1 row)
db=#
