A disk drive is disclosed comprising a disk having a host addressable area and a reserved area, an exception table stored in the reserved area, a head actuated radially over the disk to write data to the disk, and control circuitry coupled to the head. The control circuitry receives a first command from the host to write first host data into a first physical sector on the disk, wherein the first host data comprises an amount of data less than a full storage capacity of the first physical sector. The control circuitry detects an uncorrectable error while reading the first physical sector during read-modify-write operation, and indicates in the exception table that the first physical sector is a partial sector including valid and invalid logical block addresses (LBAs).