During the R12 upgrade, looks like Oracle upgrade program doesn't stop you when there are errors in FNDLOAD program. I really don't know if there is a better way to resolve this(please add comments, if you know how to resolve this), but here is what I do now.
1. go to the log directory, ie your $APPL_TOP/admin/xxxx/log
2. using the grep:
grep "ORA-" *ldt.log > ora.txt
3. check this ora.txt file,and find out which fndload failed, fix the problem and try load it again, hope there are not too much.
More details for FNDLOAD, see Oracle support note:
Tips About FNDLOAD [ID 735338.1]
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