Booby Trap - S3-E6
Corrected entry: It's a given that the Enterprise had the ability to use phasers to fire at the aceton collectors, but since they run on energy, why didn't they use photon torpedoes to destroy the collectors? They don't rely on regular energy, but explosive force to do their destructive capabilities. Even those collectors wouldn't be able to withstand a matter/anti-matter explosion of a photon torpedo without any type of shielding.
Correction: A matter/anti-matter explosion still releases energy that other collectors would use. Matter/anti-matter explosions is how they power the ship, by harnessing the power from the explosion.