Docker devicemapper (direct-lvm) metadata gets huge amount of folders

Question

Hi i have 3 node Swarm docker setup (1 manager, 2 nodes) on Centos 7. I'm using devicemapper data storage for all three VM's. The problem is that after some time folder:

/var/lib/docker/devicemapper/metadata and ../mnt

have so many files / folders they cannot be even "ls'ed". docker system prune, and docker volume prune, are not clearing antyhing.

Any ideas why it does happen and how to fix it?

Server Version: 17.06.0-ce
Storage Driver: devicemapper
 Pool Name: docker-thinpool
 Pool Blocksize: 524.3kB
 Base Device Size: 10.74GB
 Backing Filesystem: xfs
 Data file: 
 Metadata file: 
 Data Space Used: 3.055GB
 Data Space Total: 20.4GB
 Data Space Available: 17.34GB
 Metadata Space Used: 120.5MB
 Metadata Space Total: 213.9MB
 Metadata Space Available: 93.4MB
 Thin Pool Minimum Free Space: 2.039GB