Did you delete any files/folders from the GDS(Global Document Storage)?
These kind of problems occurs across the workflow processes. I suspect this is because of asynchronous jms calls.
I faced a problem something similar to this:
A webservice component was consuming lot of time to execute. So through the adminui, I terminated the task.
The next component (user task) in the workflow got executed twice with two different task Ids. miracle !!
Sometime i'm getting connection reset error with web service components. After a retry, it works well.
Anyone have more insight on this issue. I am still having issues with a failure to assign a task to user because of a JobNotFoundException