I was trying to get behavior as if my Core Data entity could have an NSMutableData attribute. To do this my NSManagedObject (called Data) had an NSData attribute and an NSMutableData ivar. My app takes sample data from a sensor and appends each data point to the data set - this is why I needed this design.
On each new data point was appended to the NSMutableData and then the NSData attribute was set to the NSMutableData.
I suspect that because the NSData pointer wasn't changing (though its content was), that Core Data did not appreciate the amount of change. Calling -hasChanged on the NSManagedObjectContext showed that there had been changes, and calling -updatedObjects even listed the Data object as having changed. But the actual data that was being written seems to have been truncated (sometimes).
To work around this I changed things slightly. New data points are still appended to NSMutableData but NSData attribute is only set when sampling is completed. This means that there is a chance that a crash might result in truncated data - but for the most part this work around seems to have solved the problem.
Caveat emptor: the bug was always intermittent, so it is possible that is still there - but just harder to manifest.