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InnoDB, What would cause: “db1/tableABC contains 6 indexes inside InnoDB, which is different from the number of indexes 5 defined in MySQL”

MySQL 5.5.24 . We have InnoDB tables that grew almost by double (from 50GB to 100GB - file-per-table enabled) in a few weeks due to a project we are working on. The tables were freshly dumped and ...