Message waiting indicator lights are set and cleared by calling the MWI on/off numbers from the directory number you want it to be set or cleared on. You can try this yourself: pick up a phone and call the MWI on/off numbers, and the light on your phone will turn on and off. This will work whether or not your phone has a corresponding mailbox in Unity.
Your voicemail system will set and clear message waiting indicators using this very same mechanism. When Unity wants to set or clear a message waiting indicator, the Unity-CM TSP (the Unity component that registers with CallManager and handles VoIP calls) simulates a call from the right extension to the MWI on/off numbers. In your CDR report, notice the "origDeviceName" column actually shows your Unity system placing the call.
Obviously, Unity will make MWI on/off calls every time it needs to change the indicator on or off. It may also refresh MWI states from time to time -- it will do this at startup, or when it loses and reestablishes contact with Exchange, or when it's commanded to do so immediately or on a scheduled basis from the Manage Integrations tool. Depending on how your system is configured, this can clutter up your CDR database.
If the clutter bothers you, I believe that you can change a service parameter in CallManager to prevent logging this sort of call into the CDR database. From CCMAdmin, go to the Service menu, to Service Parameters. Pick your publisher server out of the list, and pick the Cisco CallManager service. Look for the parameter "CDR Log Calls with Zero Duration Flag". You probably have this on; you can turn it off if you want. This is set per-server, so take the same steps to turn it off on your other CallManager servers if you have more. This will prevent zero-length calls from being stored. These are usually failed calls but I believe it will also prevent logging of MWI calls.
I can't say for sure why other phone calls you made might not be seen in the CDR database. Please note that it can take a few minutes for call records to be inserted into the CDR database you're querying, and far longer to make it to the ART database for the built-in reporting tools to analyze.
