It may seem that way if only looking at numbers. But lets look at a few other things. Uncharted 4 was released around that time too, may or june. And there was an Uncharted bundle introduced around that time. That could explain why Sony may have "over shipped" and unless we factor in exactly how many unites were sold in the month of June and July then we can't really say.
Then there is also that in July August there were reports of stock shortages especially in Japan and a few other regions. We all took that as indication that the Neo was probably just around the corner buy we got the PS4s instead.
Whatever the case, look at the Q2 shipped numbers. 3.9M, they wouldn't ship that much out if they still have more than half that number (2.5-2.7 or even 3M) just sitting on shelves. Stores just wouldn't pick them up if they are having issues getting rid of old stock.
So the fact that they shipped out 3.9M in Q3 should out your theory to rest. It's proof that the channels were never at anytime flooded.







