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I didn't know the answer to this question so I tried to do some research, and, well, I still don't know. I found a lot of unsatisfying answers but nothing that I can point to with confidence and say this is why. Which means that you're likely to have to do some testing of your own to get closer to the answer.
Depending on call volume 15 min. seems like a lot to be off by. 50 min. seems like an impossible number. I was thinking perhaps it counts the incoming and disconnect time. So while the phone is ringing until it finally disconnects from the tower. I can't imagine that adding very much time to each call but volume could be key if it is over measuring in this way.
If I were going to test to see where the added time is coming from, I would reset the timer and check it after some time before I got a call, just to see if it changes when nothing is happening. Then compare its reading to the first call that was made or received. Really that first call should tell a lot. If it is zero before the call, the call takes 5 minutes and some change but the timer shows 6 minutes and some change that would point to my theory that it is counting from the first ring to total disconnection. Rather than just the actual pick up to hang up time.
There are a lot of apps that request Phone Control, but I've always assumed that was just so the app could know if you were on the phone or if a call was coming in. I wouldn't expect them to make calls and I certainly wouldn't expect them to do anything that would increase the call timer.
Anyway thanks for creating an account. It makes communication so much easier. Plus you get your answers faster.
The only tip I saw in my search that has an outside chance of making a difference was going into Settings>Applications>Phone (you may have to enable or access your system apps to be able to see the Phone app)>Storage>Clear cache. The impression was that its a bug in the app and some bugs can be cleared by clearing the app cache or app data. For what it's worth.
Let us know what you find.