Hmm… maybe you are right, I found that bug report: Issue 38501: multiprocessing.Pool hangs atexit (and garbage collection sometimes) - Python tracker and it says it is fixed.
Also I found that: script.module.metadatautils/utils.py at master · kodi-community-addons/script.module.metadatautils · GitHub here it is imported. Is it possible it is caused by metadatautils addon?
I think I did not install it last time I used Arctic Zephyr 2 and I did not see that errors. Yesterday I reinstalled CE and tried Arctic Zephyr 2 skin one more time but this time I installed required addons manually, among others metadatautils.
Is python updated with Kodi or CE itself? How long we should wait until it will be fixed, how you think? 
and is this error problematic or I can ignore it?
Thanks for your help