I might be wrong, but I am quite sure nothing will happen if wrong person answers the phone. It just won't work.
When the phone rings and there is more than one person around to answer; they are never told who the phone is for - like when Trinity and Morpheus reach the phone booth on Train Station - whoever picks the phone goes into their own body, so there is definitely some way to detect whose consciousness is going where.
As for Agent Smith entering Bane's body, I agree with Jack's comment above, it was still Bane, just taken over by Smith, most probably the tools to detect the right consciousness weren't programmed to check for any such possession, as there has never been anything like Agent Smith ever before.