#sql-ib***.ibd files fills up the disk after a couple of hours

Question

Why are these files created? They fills up the disk on my slave server (master/slave replication)

#sql-ib219492-948768181.ibd

The slave is created via Percona xtrabackup from a master backup

xtrabackup --prepare --target-dir="$mysql_restore_dir"
xtrabackup --move-back --target-dir="$mysql_restore_dir"
rm -r $mysql_restore_dir/*
chown -R mysql.mysql $mysql_dir

mysql -u root -p$slave_pass -e "RESET MASTER;\
    SET GLOBAL gtid_purged='$gtid';\
    CHANGE MASTER TO MASTER_HOST='$master_host', MASTER_USER='repl', MASTER_PASSWORD='$master_pass', MASTER_AUTO_POSITION=1;\
    START SLAVE"

my.cnf

[mysqld]

# GENERAL #
user                           = mysql
port                           = 3306
default_storage_engine         = InnoDB
pid-file                       = /var/run/mysqld/mysqld.pid
socket                         = /var/run/mysqld/mysqld.sock

# SAFETY #
max_allowed_packet             = 16M
max_connect_errors             = 1000000
skip_name_resolve
sql_mode                       = STRICT_ALL_TABLES,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION,NO_ZERO_DATE,NO_ZERO_IN_DATE,ERROR_FOR_DIVISION_BY_ZERO
sysdate_is_now                 = 1
symbolic_links                 = 0

# DATA STORAGE #
datadir                        = /var/lib/mysql/

# BINARY LOGGING #
server_id                      = 2
log_bin                        = /var/lib/mysql/mysql-bin
log_slave_updates
expire_logs_days               = 1
sync_binlog                    = 1
log_bin_trust_function_creators= 1
binlog_format                  = ROW
slave_sql_verify_checksum      = 1

# REPLICATION #
gtid_mode                      = 1
enforce_gtid_consistency
replicate_do_db                = mydb
#super_read_only                = 1

# CACHES AND LIMITS #
tmp_table_size                 = 64M
max_heap_table_size            = 64M
query_cache_type               = 0
query_cache_size               = 0
max_connections                = 500
thread_cache_size              = 50
open_files_limit               = 65535
table_definition_cache         = 4096
table_open_cache               = 4096

# INNODB #
innodb_flush_method                 = O_DIRECT
innodb_log_files_in_group           = 2
innodb_log_file_size                = 512M
innodb_log_buffer_size              = 64M
innodb_flush_log_at_trx_commit      = 2
innodb_file_per_table               = 1
innodb_buffer_pool_size             = 1G
innodb_buffer_pool_instances        = 1
innodb_autoinc_lock_mode            = 2

# LOGGING #
log_error                      = /var/lib/mysql/mysql-error.log
log_queries_not_using_indexes  = 1
slow_query_log                 = 1
slow_query_log_file            = /var/lib/mysql/mysql-slow.log
long_query_time                = 1

basedir                        = /usr
tmpdir                         = /tmp
lc_messages_dir                = /usr/share/mysql
explicit_defaults_for_timestamp

SHOW PROCESSLIST returns