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67d34a1
(Get the code!)
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.