Comment 3 for bug 1555626

Could reproduce with PS 5.7.11-4.
Slightly changed test.sh and added alter encryption:

root@percona-XPS-15:~# cat test.sh
#!/bin/bash

echo "drop table if exists db1.sb1" | /opt/percona-5.7.11-4/bin/mysql -u root -pBaku12345# --socket=/opt/percona-5.7.11-4/datadir/mysqld.sock --port=5711
echo "create table db1.sb1 as select id,c from db1.sbtest1 where id < 150000;"| /opt/percona-5.7.11-4/bin/mysql -u root -pBaku12345# --socket=/opt/percona-5.7.11-4/datadir/mysqld.sock --port=5711
echo "alter table db1.sb1 encryption='Y'" | /opt/percona-5.7.11-4/bin/mysql -u root -pBaku12345# --socket=/opt/percona-5.7.11-4/datadir/mysqld.sock --port=5711
echo "create unique index ix on db1.sb1 (id)" | /opt/percona-5.7.11-4/bin/mysql -u root -pBaku12345# --socket=/opt/percona-5.7.11-4/datadir/mysqld.sock --port=5711
sleep 1
echo "drop table if exists db2.sb1" | /opt/percona-5.7.11-4/bin/mysql -u root -pBaku12345# --socket=/opt/percona-5.7.11-4/datadir/mysqld.sock --port=5711
echo "create table db2.sb1 as select id,c from db2.sbtest1 where id < 150000;" | /opt/percona-5.7.11-4/bin/mysql -u root -pBaku12345# --socket=/opt/percona-5.7.11-4/datadir/mysqld.sock --port=5711
echo "alter table db2.sb1 encryption='Y'" | /opt/percona-5.7.11-4/bin/mysql -u root -pBaku12345# --socket=/opt/percona-5.7.11-4/datadir/mysqld.sock --port=5711
echo "create unique index ix on db2.sb1 (id)" | /opt/percona-5.7.11-4/bin/mysql -u root -pBaku12345# --socket=/opt/percona-5.7.11-4/datadir/mysqld.sock --port=5711

Take Backup:

root@percona-XPS-15:/usr/local/xtrabackup/bin# cat run_backup.sh
./xtrabackup --defaults-file=/opt/percona-5.7.11-4/my.cnf --backup --datadir=/opt/percona-5.7.11-4/datadir --target-dir=/home/backup_dir/full/ --user=root --password=Baku12345# --socket=/opt/percona-5.7.11-4/datadir/mysqld.sock --port=5711 --no-version-check --keyring-file-data=/opt/percona-5.7.11-4/keyring/keyring --server-id=0

sleep 10

./xtrabackup --defaults-file=/opt/percona-5.7.11-4/my.cnf --backup --target-dir=/home/backup_dir/inc/inc1 --incremental-basedir=/home/backup_dir/full --datadir=/opt/percona-5.7.11-4/datadir --user=root --password=Baku12345# --socket=/opt/percona-5.7.11-4/datadir/mysqld.sock --port=5711 --no-version-check --keyring-file-data=/opt/percona-5.7.11-4/keyring/keyring --server-id=0

sleep 10

./xtrabackup --defaults-file=/opt/percona-5.7.11-4/my.cnf --backup --target-dir=/home/backup_dir/inc/inc2 --incremental-basedir=/home/backup_dir/inc/inc1 --datadir=/opt/percona-5.7.11-4/datadir --user=root --password=Baku12345# --socket=/opt/percona-5.7.11-4/datadir/mysqld.sock --port=5711 --no-version-check --keyring-file-data=/opt/percona-5.7.11-4/keyring/keyring --server-id=0

sleep 10

./xtrabackup --defaults-file=/opt/percona-5.7.11-4/my.cnf --backup --target-dir=/home/backup_dir/inc/inc3 --incremental-basedir=/home/backup_dir/inc/inc2 --datadir=/opt/percona-5.7.11-4/datadir --user=root --password=Baku12345# --socket=/opt/percona-5.7.11-4/datadir/mysqld.sock --port=5711 --no-version-check --keyring-file-data=/opt/percona-5.7.11-4/keyring/keyring --server-id=0

Prepare backups:

root@percona-XPS-15:/usr/local/xtrabackup/bin# cat prepare_backup.sh
./xtrabackup --defaults-file=/home/backup_dir/full/backup-my.cnf --prepare --apply-log-only --target-dir=/home/backup_dir/full --keyring-file-data=/opt/percona-5.7.11-4/keyring/keyring --server-id=0

sleep 10

./xtrabackup --defaults-file=/home/backup_dir/full/backup-my.cnf --prepare --apply-log-only --target-dir=/home/backup_dir/full --incremental-dir=/home/backup_dir/inc/inc1 --keyring-file-data=/opt/percona-5.7.11-4/keyring/keyring --server-id=0

sleep 10

./xtrabackup --defaults-file=/home/backup_dir/full/backup-my.cnf --prepare --apply-log-only --target-dir=/home/backup_dir/full --incremental-dir=/home/backup_dir/inc/inc2 --keyring-file-data=/opt/percona-5.7.11-4/keyring/keyring --server-id=0

sleep 10

./xtrabackup --defaults-file=/home/backup_dir/full/backup-my.cnf --prepare --target-dir=/home/backup_dir/full --incremental-dir=/home/backup_dir/inc/inc3 --keyring-file-data=/opt/percona-5.7.11-4/keyring/keyring --server-id=0

Result:

InnoDB: Doing recovery: scanned up to log sequence number 2910532608 (52%)
InnoDB: Ignoring data file './db2/sb1.ibd' with space ID 113. Another data file called ./db2/#sql-2cf2_5d.ibd exists with the same space ID.
InnoDB: Cannot rename './db2/#sql-2cf2_5d.ibd' to './db2/sb1.ibd' for space ID 113 because the target file exists. Remove the target file and try again.
InnoDB: Cannot replay file rename. Remove either file and try again.
InnoDB: Plugin initialization aborted at srv0start.cc[2206] with error Generic error
xtrabackup: innodb_init(): Error occured.