Well, this isn't the first time we have a Cyberman go against it's programming because of emotion -
In Doomsday a cyberman/woman (Yvonne) goes against her programming - and disobeys orders - and a tear of oil leaks out of her eye. Potentially in both Danny and Yvonnes case - they were so determined NOT to be "upgraded" that they were able to interfere with the process.
However it still has not been explained - how exactly - the digital dead minds can "feel" what happens to their physical bodies - providing of course that wasn't just a lie.
Nor has it been explained what "missy" has to do with Clara being the impossible girl. It is explained why the Doctor and the current Clara were destined to meet - but not what that has to do with the previous 2 Clara's......
Biting the hand that feeds IT
