I have this problem as well. It occurs regardless of whether my 4TB My Passport Pro is connected to the thunderbolt port of my Thunderbolt Display or connected directly to my new Macbook Pro running MacOS X 10.9.4.
It doesn’t always happen, but when it does happen it is always after the computer has entered sleep mode.
Plugging directly to the Thunderbolt port on the MBP kind of defeats the purpose of having the thunderbolt display as a docking station. And it doesn’t fix the problem anyway.
I’m not sure if this is a WD problem or a OS X driver issue. So far there has been no loss of data.
