Drivers Side Axle Shaft Or Transmission issue.

I had my 1990 Nissan Stanza GXE with a 2.4L 4-cyl. Engine, Automatic (Locking transmission) carried in to have the tires rotated and the tire dealer and they said that the boot on the driver’s side axle shaft was torn so they replaced it. After 3 weeks the front end of the vehicle started shaking when you decelerate. Once you accelerate the shaking goes away. The tire dealer which replaced the axle shaft could not get the axle out of the transmisson so they carried the transmission to a local transmission shop and they said that the shaft broke off in the transmission and it was because of the transmission and not the shaft. Is this possible, and what questions should I ask or what should I look for to make sure I am not being taken advantage of?