When ZEKE is hijacked by Paz and she reveals her true colors and allegiance, Big Boss seemed to not even recognize Cipher at all. Even when Paz mentions the whole Zero and Big Boss splitting apart story, the first reaction Big Boss gives is a confused "huh?". Does anyone know why Big Boss would seem to not even recognize Cipher even when Paz mentioned Zero and Big Boss splitting apart? I mean, in a way, it does contradict EVA's account to the formation of the Patriots and by extension, the plot of MGS4. Plus, it somewhat implies that Big Boss never even formed the Patriots at all, which makes it even more confusing.
If anyone can explain this, it should be good. Personally, I do believe that MGS4 is still canon, as is MPO, but I often have to use this arguement to people who claim that MPO is not canon anymore or at the very least a canon sidegame that should be forgotten because their arguements can be countered with things like this that would make MGS4 non canon or at least a canon sidegame that should be forgotten.