I confirm this problem for PXC 5.6.20. When the innodb_log_group_home_dir points to a directory inside innodb_data_home_dir - xtrabackup-v2 SST method fails.

percona1 mysql> select @@version,@@version_comment;
+----------------+---------------------------------------------------------------------------------------------------+
| @@version      | @@version_comment                                                                                 |
+----------------+---------------------------------------------------------------------------------------------------+
| 5.6.20-68.0-56 | Percona XtraDB Cluster (GPL), Release rel68.0, Revision 888, WSREP version 25.7, wsrep_25.7.r4126 |
+----------------+---------------------------------------------------------------------------------------------------+
1 row in set (0.00 sec)

percona1 mysql> show variables like 'innodb_%dir%';
+--------------------------------+-------------------+
| Variable_name                  | Value             |
+--------------------------------+-------------------+
| innodb_data_home_dir           | /data/innodb      |
| innodb_log_arch_dir            | /data/innodb/logs |
| innodb_log_group_home_dir      | /data/innodb/logs |
| innodb_max_dirty_pages_pct     | 75                |
| innodb_max_dirty_pages_pct_lwm | 0                 |
| innodb_undo_directory          | /data/innodb      |
+--------------------------------+-------------------+
6 rows in set (0.00 sec)

in my.cnf:
[sst]
streamfmt=xbstream
sst_special_dirs=1

Forced SST to percona1 node:

WSREP_SST: [INFO] Proceeding with SST (20141018 10:58:14.247)
WSREP_SST: [INFO] Cleaning the existing datadir and innodb-data/log directories (20141018 10:58:14.250)
removed `/data/innodb/ibdata1'
removed `/data/innodb/logs/ib_logfile1'
removed `/data/innodb/logs/ib_logfile0'
removed directory: `/data/innodb/logs'
removed `/data/innodb/undo002'
removed `/data/innodb/undo001'
(...)
WSREP_SST: [INFO] Evaluating socat -u TCP-LISTEN:4444,reuseaddr stdio | xbstream -x; RC=( ${PIPESTATUS[@]} ) (20141018 10:58:14.295)
2014-10-18 10:58:29 18105 [Note] WSREP: 1.0 (percona2): State transfer to 2.0 (percona1) complete.
2014-10-18 10:58:29 18105 [Note] WSREP: Member 1.0 (percona2) synced with group.
WSREP_SST: [INFO] Compressed qpress files found (20141018 10:58:29.062)
WSREP_SST: [INFO] Decompression with 2 threads (20141018 10:58:29.067)
WSREP_SST: [INFO] Evaluating find /data/myisam//.sst -type f -name '*.qp' -printf '%p\n%h\n' | xargs -n 2 qpress -T2d (20141018 10:58:29.071)
WSREP_SST: [INFO] Removing qpress files after decompression (20141018 10:58:29.646)
WSREP_SST: [INFO] Preparing the backup at /data/myisam//.sst (20141018 10:58:29.663)
WSREP_SST: [INFO] Evaluating innobackupex --no-version-check  --apply-log $rebuildcmd ${DATA} &>${DATA}/innobackup.prepare.log (20141018 10:58:29.666)
WSREP_SST: [INFO] Moving the backup to /data/myisam/ (20141018 10:58:34.923)
WSREP_SST: [INFO] Evaluating innobackupex --defaults-file=/etc/my.cnf --no-version-check   --move-back --force-non-empty-directories ${DATA} &>${DATA}/innobackup.move.log (20141018 10:58:34.927)
WSREP_SST: [ERROR] Cleanup after exit with status:1 (20141018 10:58:35.524)
WSREP_SST: [INFO] Removing the sst_in_progress file (20141018 10:58:35.528)
2014-10-18 10:58:35 18105 [ERROR] WSREP: Process completed with error: wsrep_sst_xtrabackup-v2 --role 'joiner' --address '192.168.99.2:4444' --auth 'root:cmon' --datadir '/data/myisam/' --defaults-file '/etc/my.cnf' --parent '18105'  '' : 1 (Operation not permitted)
2014-10-18 10:58:35 18105 [ERROR] WSREP: Failed to read uuid:seqno from joiner script.
2014-10-18 10:58:35 18105 [ERROR] WSREP: SST failed: 1 (Operation not permitted)
2014-10-18 10:58:35 18105 [ERROR] Aborting

when I remove innodb_log_group_home_dir setting, or point to the same dir as innodb_data_home_dir - all works well.