User blog comment:Weedle McHairybug/So, why did Big Boss react with confusion in regards to Cipher? (Spoilers)/@comment-1504072-20100825205834

Big Boss always repeats words as questions, it doesn't necessarily mean he didn't recognize to whom she was referring. His confused expression later could just be referring to the whole situation in general (i.e. how Paz's hijacking of ZEKE was a direct result of his splitting from Zero's group).