When playing as Lucas during the coverup, don't hide the knife. Wash your hands, then leave the bathroom. Pay your bill, leave from the front door, and either take a cab (left from the exit and up the street, then right) or the subway to flee the crime scene.
As Carla, find the knife in the bathroom (it's by the urinals), then complete the conversation with Kate the waitress. Leave the diner via the front door, and you'll be able to examine a small puddle of blood between the door and the car. The trophy will unlock soon after.
Solution taken from PlayStation Trophies:
https://www.playstationtrophies.org/game/indigo-prophecy/tro...