Please check the tools.cfg file and make sure TableOwner parameter is correct for the datasource you are using. For example, if you are using a local database make sure parameter TableOnwer under [Local] section of tools.cfg file is set with the correct tableowner username as below:
I have also faced the same type error/issue while performing the Apply/Activate on table.
I have entered the sequence number against each extension coulumn and did apply activate on base table. Later created Attribute Mapping against respected EIM table.
Then while apply/activating on EIM table queries for only those selected extended column and did Apply-Activate, it worked.
Hope the solution will help you out on apply activating without error.