Hi, Thanks for test case. I was able to reproduce the same with PS 5.6.21 and Xtrabackup 2.2.7

root@desktop:~# xtrabackup --version
xtrabackup version 2.2.7 based on MySQL server 5.6.21 Linux (x86_64) (revision id: )
root@desktop:~# 

nilnandan@desktop:~$ mysql -uroot -p
Enter password: 
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 47
Server version: 5.6.21-70.1 Percona Server (GPL), Release 70.1, Revision 698

...
Type 'help;' or '\h' for help. Type '\c' to clear the current input statement.

mysql> 
mysql>  SELECT @@version, @@version_comment;
+-------------+--------------------------------------------------+
| @@version   | @@version_comment                                |
+-------------+--------------------------------------------------+
| 5.6.21-70.1 | Percona Server (GPL), Release 70.1, Revision 698 |
+-------------+--------------------------------------------------+
1 row in set (0.00 sec)

mysql> create database include00;
Query OK, 1 row affected (0.00 sec)

mysql> create database exclude00;
Query OK, 1 row affected (0.00 sec)

mysql> use include00
Database changed
mysql> 
mysql> create table table00 (id bigint unsigned primary key auto_increment, data varchar(40)) engine=innodb character set = utf8;
Query OK, 0 rows affected (0.01 sec)

mysql> insert into table00 (data) values ('abcdnedlkjsdlkjasdlkj alkjdlaskjldkjasdl');
Query OK, 1 row affected, 0 warning (0.00 sec)

mysql> select * from table00;
+----+------------------------------------------+
| id | data                                     |
+----+------------------------------------------+
|  1 | abcdnedlkjsdlkjasdlkj alkjdlaskjldkjasdl |
+----+------------------------------------------+
1 row in set (0.00 sec)

mysql> insert into table00 (data) select data from table00;
Query OK, 1 row affected (0.01 sec)
Records: 1  Duplicates: 0  Warnings: 0

...
mysql> insert into table00 (data) select data from table00;
Query OK, 8388608 rows affected (33.35 sec)
Records: 8388608  Duplicates: 0  Warnings: 0


----- Take a backup with this. 

root@desktop:~# innobackupex --user=root --password=root --databases='include00' /home/nilnandan/backup

InnoDB Backup Utility v1.5.1-xtrabackup; Copyright 2003, 2009 Innobase Oy
and Percona LLC and/or its affiliates 2009-2013.  All Rights Reserved.

This software is published under
the GNU GENERAL PUBLIC LICENSE Version 2, June 1991.
....

Simultaneously, ran truncate
mysql> truncate table excluded_table00;
Query OK, 0 rows affected (0.34 sec)


Before --apply-log

root@desktop:~# tree -a /home/nilnandan/backup/2014-12-30_11-57-31/
/home/nilnandan/backup/2014-12-30_11-57-31/
├── backup-my.cnf
├── ibdata1
├── include00
│   ├── db.opt
│   ├── table00.frm
│   └── table00.ibd
├── xtrabackup_checkpoints
├── xtrabackup_info
└── xtrabackup_logfile

1 directory, 8 files
root@desktop:~# 

-- After --apply-log

root@desktop:~# tree -a /home/nilnandan/backup/2014-12-30_11-57-31/
/home/nilnandan/backup/2014-12-30_11-57-31/
├── backup-my.cnf
├── exclude00
│   └── excluded_table00.ibd
├── ibdata1
├── ib_logfile0
├── ib_logfile1
├── include00
│   ├── db.opt
│   ├── table00.frm
│   └── table00.ibd
├── xtrabackup_checkpoints
├── xtrabackup_info
└── xtrabackup_logfile