Right now, I'm using Carbon Copy Cloner to clone the HDD that came with my Late 2011 MBP, (running OS X 10.8.4) onto a new Crucial M500 960GB SSD. I've got the SSD docked in a brand new Seagate Thunderbolt Adapter, connected with an Apple Tbolt cable to my MBP. All the connections are solid.
The SSD has self-ejected no less than 10 times so far. I have turned off WiFi and disabled any program that runs at startup, thinking that something was changing the information on the drive. As I type, it just happened again...
Each time it happens, messages pop up saying "CCC aborted the task because the destination volume disappeared. Please reconnect the volume and try the task again". AND "The disk was not ejected properly. If possible, always eject a disk before unplugging it or turning it off." AND "The backup task was aborted because the destination volume's mountpoint changed. Try the task again. Avoid making any changes to the source and destination volumes during the backup task." (It just happened again.)
Fortunately, each time I have to restart the task, the cloning software moves very quickly through the data it has already transfered. That gives me hope that sometime tonight I'll be finished with this project...
Bottom line - It happens with Thunderbolt equipment as well.