The trophies that do not work after patch 1.09 are:
Decimation (destroy 500 machines)
Hasta La Vista Baby (destroy 30 seekers)
Yippee-Ki-Yay (destroy 15 harvesters)
Say Hello To My Little Friend (destroy 15 Tanks)
Explorer (discover 50 locations)
Tunnel Rat (discover 5 bunkers)
Kill Switch (destroy 10 relay beacons)
Go-Getter (complete 25 world events)
Fashionista (collect 200 items of apparel) has been fixed with patch 1.10 and works retroactively as was promised.