Comment 0 for bug 1062684

If in your [mysqld] section of my.cnf, this is set:
innodb_data_file_path = ibdata1:2000M;ibdata2:10M:autoextend

innobackupex cannot apply incremental backup:
121005 21:31:47 innobackupex: Starting ibbackup with command: xtrabackup_55 --defaults-file="/backups/full/2012-10-05_21-22-00/backup-my.cnf" --defaults-group="mysqld" --prepare --target-dir=/backups/full/2012-10-05_21-22-00 --apply-log-only --incremental-dir=/backups/incremental/2012-10-05_21-23-37

innobackupex --apply-log --redo-only --incremental-dir=/backups/incremental/2012-10-05_21-23-37 /backups/full/2012-10-05_21-22-00
xtrabackup_55 version 2.0.3 for Percona Server 5.5.16 Linux (x86_64) (revision id: 470)
incremental backup from 416883306 is enabled.
xtrabackup: cd to /backups/full/2012-10-05_21-22-00
xtrabackup: This target seems to be already prepared.
xtrabackup: xtrabackup_logfile detected: size=2097152, start_lsn=(416883306)
xtrabackup: Temporary instance for recovery is set as followings.
xtrabackup: innodb_data_home_dir = ./
xtrabackup: innodb_data_file_path = ibdata1:2000M;ibdata2:10M:autoextend
xtrabackup: innodb_log_group_home_dir = /backups/incremental/2012-10-05_21-23-37
xtrabackup: innodb_log_files_in_group = 1
xtrabackup: innodb_log_file_size = 2097152
121005 21:31:47 InnoDB: Using Linux native AIO
InnoDB: Error: data file ./ibdata1 is of a different size
InnoDB: 128000 pages (rounded down to MB)
InnoDB: than specified in the .cnf file 2000 pages!
xtrabackup: Could not open or create data files.
xtrabackup: If you tried to add new data files, and it failed here,
xtrabackup: you should now edit innodb_data_file_path in my.cnf back
xtrabackup: to what it was, and remove the new ibdata files InnoDB created
xtrabackup: in this failed attempt. InnoDB only wrote those files full of
xtrabackup: zeros, but did not yet use them in any way. But be careful: do not
xtrabackup: remove old data files which contain your precious data!
xtrabackup: error: xb_data_files_init() failed witherror code 11
innobackupex: Error:
innobackupex: ibbackup failed at /usr/bin/innobackupex line 378.

Workaround:
Install xtrabackup-2.0.1 to apply incremental backup