I came across the same issue. This warning is thrown when calling [NSStream close] upon receiving an EAAccessoryDidDisconnectNotification. There should be also some data exchange between the two devices just before the disconnection.
Breaking on _NSLockError will show that at the moment the object is deallocated, some of the threads spawned by the external accessory framework are waiting on conditions. One of those certainly waits on the condition that is being freed, which explains the warning thrown on the console.
I also noticed that the number of threads created by the external accessory framework keeps on growing each time the accessory disconnects then connects, and they seem to be just leaking.
It seems to me that somehow, the external accessory framework does not properly free the resources it allocates, which results in a lot of mess. One of the subsequent effects of this are crashes that happen inside one of those leaked threads during a call to OSAtomicCompareAndSwap64.
I managed to reproduce the issue using a basic sample in which the streams are scheduled on the main thread to avoid any thread management inside the application. I believe it's an accessory management bug on iOS 6 that Apple should be aware of. I'll report it and wait for what they have to say.
Meanwhile, I wonder if anyone of you guys has managed to make any progress on this.
Thanks,