Because the villain doesn't give fucks about heroic morality. Far easier to let someone do the heavy lifting for you and then take em out when they are weak. See in FF4 during the Sealed Cave segment where you had to go through countless amounts of Phoenix Downs and Ethers and then fight an annoying as fuck boss, only to have Kain snatch it from you via Golbez control. Same with FF7 and the Black Materia, Sephiroth couldn't get it due to the puzzle, so he simply let the heroes solve it for him. Even FF6 did it with the Esper slaughter at Thamasa where their whole plan was to deceive the protagonists into making peace with them to lure them into the open so Magicite could be collected and reduced opposition keeping them away from the sealed gate.
Even SaGa 2 did this with Apollo using the characters you met as hostages so he can collect all the MAGI/Relics in your possession.
Why do the work when your opponent can do it for you?