There are 4 parts to this Side Mission. If done in the post-game, enter/exit a nearby building first before each encounter.
Part 1 - After leaving the Courthouse early on, he's across the street on top of the building to your right. This is when you can get the Catch Trophy as well. You should be able to see him there by clicking on your controller.
Part 2 - After leaving the Steel Mill for the first time you should be facing the ocean, so go left and you should see a Ferris Wheel. Go to the top of the Ferris Wheel for the second signal.
Part 3 - After interrogating Quincy Sharp and the cutscene ends, turn around to see that he's across the street on top of the building for the 3rd signal. He should be slightly to your right and slightly above you.
Part 4 - After saving Vicky Vale, turn around and look to the building across the street for his next-to-final location. After getting the final signal, you'll be asked to line up the symbols to reveal the location of the final symbol. The 4 dots represent the 4 places where you've met him so far. The final location is a side of the Church, where the full symbol is waiting to be scanned. Go there and scan it for the final meeting and the Trophy.
Thanks to Xx Overkill VR over at x360a.org for this photo
I missed him the first time outside of the courthouse in the beginning of the game as well but I went back after meeting up with Joker and he's still there. He'll only show up after beating certain parts of the main story. You can't just go from location to location and get the trophy. You have to play the game and do it while you're playing. I tried gliding from place to place where he is suppose to be and it didn't work.
His locations are the following: right across from the court house on a building called Park Row. At the very very top of the Ferris Wheel. The building across from the GCPD and close to the Museum. The building thats right beside the subway station.
Forgot to mention that after you find Azrael at all four locations you need to adjust the map that he gives you by zooming out and turning it around a bit until it covers all four locations where you met him. It provides you with the last location, meet up with him again, then you get the trophy.