So you have not upgraded the tablespaces. What is important to remember is Postgres uses numbers to keep track of relations. Part of the upgrade process involves changing the numbers that point at relations. By manually dropping a 9.0 tablespace into a 9.3 data directory you have broken that system. You need to let pg_upgrade do the translation. See my previous message below for a possible solution:
Sorry, I may not have been to clear on my explenation, pg_upgrade creates the 9.3 data directories inside the tablespace folders and those are the ones I moved. So pg_upgrade finishes it's job.