The other very common possibility is that it's what's called a "ghost shift" where the factory runs a whole production run on a possibly overnight work shift, creates a batch of product for sale to third parties, and then resumes their legit-for-transfer-to-apple production run the next morning. Happens with all sorts of electronics manufacturing in mainland china.
This does not necessarily mean that the ghost shift products go through absolutely the same level of QC that the main production run gets, but I wouldn't call them counterfeit.