The issue is that the Yosemite upgrade moves everything in /usr to a temporary folder during the process and then of course moves back anything it didn't have to upgrade. If you have a lot of files, that can take extra time and if you have insufficient disk space, the upgrade may fail or data might be lost. You should move any such files elsewhere before the upgrade.
As Pavel noted, this affects Kerio Connect if the Kerio Connect message store is located in a default location (/usr/local/kerio/mailserver/store).
He also notes that Yosemite doesn't install Java by default. You need that for Kerio Connect. It's simple to get: type "java" in a Terminal window and a browser window will open for the download. You need the JDK, not JRE unless Oracle has fixed the problem seen earlier.
I experienced a different issue. I run as a non-administrator account (no sudo privilege). The uprade worked, but could not finish upon reboot until I logged into an administrative account.