You're seeing a secondary validation failure, which is almost always a sign of a firewall problem (either yours or regional). Occasionally, but rarely, this is a sign of DNS server issues.
@griffin thanks for welcome I've disabled all firewalls in one server including ISP's firewall. Nothing changed. I believe thats a DNS server issue too but can't find a way to fix it or define the exact problem.
I ve contacted ISP they have no idea either. As far as we know there are several ISPs from Turkey having same problem with different users. I am the only one having this problem with my ISP
Not sure but seems like this is not an issue caused by my DNS settings which never changed and was working couple days ago.
Well then you could wait for the problem to go away (much as it came - mysteriously).
OR
You could add some DNS servers far outside of your country/problem area.
There are plenty of global DNS service providers and some will even do it for free.
I can personally recommend:
OR
Host your own additional DNS server in any cloud type service (but outside the problem area).
I was planing that but not sure if that will work since validation looks for A record and it will point same IP address. Is it a lookup problem or is something blocking validation requests.
Created zone for domain in a different datacenter with same DNS settings
Added A record points to my problematic server
Changed nameserver's to other server
Installed SSL on my server. Success.
After this i've changed NS records back to my server and able to work with domain also able to renew SSL through auto installer UI
So now the question is why Letsencrypt can perform a DNS lookup for A record on my server. I've checked most known web sited for my record all works fine except MXToolbox.
MXToolbox result are a bit confusing too, may throw an error "Not able to get a response from name servers within timeframe"
After bunch of tests I made sure that the problem is not on my settings. Make ISP to check blockings again. They've changed some rules which i'm not sure what they have done but everything works fine now.
Thanks for everyone took time to reply and help me.