The Savage Curtain
CHEKOV [OC]: Bridge to Transporter room. One minute to overhead position.
SCOTT: Locked on to something. Does that appear human to you, Mister Spock?
SPOCK: Fascinating. For a moment, it appeared almost mineral. Like living rock with heavy fore claws. It's settling down now to completely human readings.
SCOTT: We can beam it aboard anytime now, sir.
...
MCCOY: Just what was it you locked onto before you beamed him aboard?
SCOTT: You heard Mister Spock yourself. Mineral he called it, like living rock.
MCCOY: And that became Lincoln?
SCOTT: I couldn't tell. It may have been another figure down there standing by. What do you make of it?
MCCOY: I'm not quite sure.
The Enterprise Incident
KIRK: Mister Chekov, there's only one Vulcan aboard that ship. He should be easy enough to locate.
CHEKOV: Romulans and Vulcans appear to read almost exactly alike. There is just a slight difference which. Got him, sir.
KIRK: Feed the co-ordinates to the transporter room on the double. Have them prepare to beam him aboard on my signal.
UHURA: Captain Kirk. Mister Scott is on the intercom for you, sir.
KIRK: Go ahead, Scotty.
.. .
CHEKOV: Sir, transporter room has the co-ordinates and is ready for beaming.
KIRK: Transporter room, beam Mister Spock aboard.
Apparently TOS era transporters did have the ability to distinguish what they were beaming up. Or, at least, with assistance from the bridge science station. Since Savage Curtain comes later, perhaps there was an upgrade.
