It's always sorta bothered me on science fiction movies and TV shows, where some sort of matter transporter device always manages to readily distinguish between which matter belongs to the person and which just happens to be nearby. Oh - and miraculously, recognizes clothing and things the person's holding as transport-marked, also.
Seems to me that even if you imagine that you could somehow code for biological entities such that a transporter would recognize the physical entity as a unit and not, you know, the floor beneath the transporter pad, etc., there'd be no particular way to recognize clothing, or the communication device the person's holding, etc.
In fact, it strikes me as weirdly analogous to the problem of spam-recognition: while various algorithms do a reasonable job of recognizing much spam as spam, it's still not as accurate as human eyeballs in spotting out obvious spam (though it's much, much quicker and less prone to succumbing to sheer tedium).
I think it'd be much more believable if a transporter device were less physics-based and more a matter of extreme mental discipline, the sort of thing that takes years of intensive training for the transportee to focus on exactly and only what needs to be transported - sort of a yogic discipline scenario.
Of course, I read very little SF these days...so far all I know, a million stories have taken up exactly this concept.