Trophy pickups in Thomas was Alone seems to not spawn until you've finished the game - they show up as small black boxes that almost go in the design of the background.
1.8 After getting over the two puddles of water and falling a level down, you'll meet a hurdle where you need to let Thomas and John help Chris getting up - only John can reach the trophy here after you've helped the other guys.
1.9 After using the elevators, the trophy is at the top right. Use John to grab it - it might take some tries before reaching it, but no foul and harm, easy to get back up.