This is one of three different trophies that require you to collect clue bottles. The earliest you can obtain any, or all, of these three is found during the first level, when Dimitri and the Clockwerk Feathers are your target. All of the clue bottles will be found outside, not inside where you might end up going for some missions. Check on top of roofs, in corners, on balconies, and make sure you sweep around the edges of the map, as there is a second part to the map that might be separated by a gate (on one side, at least). You can jump over it near an edge, or go the opposite direction (where Murray will be breaking an alarm box).