There has been talk within WWE for about 6-8 weeks that John Cena is still having problems with his shoulder but is now having more problems with his neck. These are longterm nagging issues that Cena has been dealing with.
It was also said that there are a lot of people within WWE keeping an eye on Cena to see where he will be going forward in regards to acting and not wrestling as much.
There are also people within WWE who say Cena appears to be in pain and they believe Cena has slowed down physically in the way he moves.
Source: WrestlingInc.com