The issue is mainly because a large number of Accor properties still don't use hotel link. For the properties that don't use hotel link, when you make a reservation via the Accor website, the Accor system emails the details of the booking to the hotel. The hotel then manually inputs the reservation into their in-house system. Often the Accor member number may get missed etc. resulting in a guest not getting their status benefits and also not getting their stay credited.
On the topic of stay crediting, in properties that aren't using hotel link, the stays posting process is a manual process. Generally the front office manager is responsible for doing it.
This is not just an Accor issue - many of the independent properties that you find on booking.com, expedia etc. also operate in this way. You would be amazed at how much manual work there is when it comes to accommodation reservations.