Bearing Vs. Differential Bearing

I took my 2002 Mini Cooper to a Transmission Rebuild guy a year and half ago. He replaced the clutch plate and the bearings in the transaxle. A couple of months ago it started making cavitating sounds. So, I took it back to the guy to have it checked out. Now he is saying that the differential bearing is going out, causing the cv joint to wobble, and I did not have the differential bearing replaced last time, so it is not covered under the warranty he places on his work.
Can someone tell me what the difference is between the bearings in the transaxle and differential bearings? Don't trust this guy and want to know if he is not telling me the truth.