This trophy is story-related and cannot be missed via normal campaign progression.
This sequence is host to the one missable trophy in the game. Make sure you grab the trophy
Flyswatter before you finish this sequence.
You will first have to test the flying machine that Leonardo has built. You can quickly crash into a wall or building to move the sequence along. Eventually you will get to use the flying machine for a second time and that is when you can get the trophy mentioned above.
When you reach the Palazzo's rooftop you must remain incognito and kill your target. If you get seen, the checkpoint will plop you back on the roof, so at least you won't have to fly across Venice again.