This trophy appears to be a little glitchy.
You'll have to use the groovitron on all enemies throughout the game including different versions of enemies (such as the four different versions of warbots). Also be sure to use it on the Sewer Sharks (the green fish), both swimming and not, as well as the tentacles on the train in Aleero City.
If you don't get it on the first playthrough, your progress will carry over into the first Challenge mode. Note that upon beginning your second consecutive challenge mode playthrough, all previous progress appears to be lost, and from that point forward, you'll have to use the groovitron on every enemy in a single playthrough.
This trophy CAN be unlocked while cheats are active (these will appear under the Extras menu after obtaining all of the gold bolts). You won't earn weapon experience while cheats are active, but unlimited ammo is obviously very helpful for this trophy.