We have exactly the same problem. We cannot use Xtrabackup 2.3.1-beta1 on a MySQL slave in a GTID enabled replication setup. Executing:
FLUSH NO_WRITE_TO_BINLOG ENGINE LOGS
adds an errant transaction and we start getting notifications from our monitoring system. At this point we have to fix the "Executed_Gtid_Set" value on the slave or inject empty transactions on all other servers. This is not easy to do, so for now we decided against using Xtrabackup on MySQL slaves.
We have exactly the same problem. We cannot use Xtrabackup 2.3.1-beta1 on a MySQL slave in a GTID enabled replication setup. Executing:
FLUSH NO_WRITE_TO_BINLOG ENGINE LOGS
adds an errant transaction and we start getting notifications from our monitoring system. At this point we have to fix the "Executed_Gtid_Set" value on the slave or inject empty transactions on all other servers. This is not easy to do, so for now we decided against using Xtrabackup on MySQL slaves.