Limitation of Debugger:- Debugging inside of an atomic scope. You cannot set a breakpoint on shapes inside of an atomic scope or an orchestration that is defined as Atomic.
Fur further details please refer this: http://msdn.microsoft.com/en-us/library/aa953746(BTS.20).aspx
Alternative would be to writing information to the Event log or some file for testing purpose temporarily. or use the Long Running scope.