This error happens when your code (or MagicalRecord) retains an object that is deleted by CoreData in a managed object context, usually on another thread. I would make sure I am not storing temporary objects or objects that may be deleted as properties, in collections, etc. Because you mentioned you don't, I would make sure I don't have threading code that might be out of sync, and ultimately, I would make sure MagicalRecord doesn't have some threaded background deletes or faux garbage collection for the one-to-many relationship classes or something of that sort that could be causing the issue.
As a solution you could check for fault objects manually to avoid the crashes. Look at this question for ways to do that: How can I tell whether an `NSManagedObject` has been deleted?
Sorry if this is too generic, but without seeing your application it is hard to say why exactly you are getting the error.