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I agree with Michael that this problem has something to do with concurrent processes. I guess it has something to do with GIT pooling? The solution that worked for me was switching to Jenkins Credentials! Previously, I did not use credential stored in Jenkins. Since I stored the GIT credentials in Jenkins and I set those credentials in GIT plugin, all works OK! So far, I experienced only one fetch timeout with the same error as before and sure enough, there was multiple instances of git running at the same time. Once I killed them, all operations returned back to normal.
In my opinion, there is something wrong either in Jenskin or GIT plugin. A question worth of a million is, what could be a reason of such behavior? In any case, switching to Jenkins Credentials seems minimize the error rate to minimum.