InnoDB compares column names case sensitively, while according to Storage Engine API column names should be compared case insensitively. This can cause FRM and InnoDB data dictionary to go out of sync:

CREATE TABLE t1 (D INT) ENGINE=innodb;

INSERT INTO t1 VALUES (10);

ALTER TABLE t1 MODIFY COLUMN d INT;

ALTER TABLE t1 ADD INDEX (d);

DROP TABLE t1;