EDIT : For some reason this achievement can be glitched. Some players can unlock this without problem, other had to defeat more than 100 enemies and the worst case is that the achievement simply doesn't unlock.
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This is easily done with the boss on Lagoon City Zone Act 1.
This boss spawns pond skaters enemies, and if you hit the boss more than 2 times, it will stop spawning enemies.
As Knuckles, tap
for jump and push
again (and hold) for glide.
Try to glide as low as possible and near the ground to hit most of the enemies. Sometimes you will hit a jumping enemy and that will stop your gliding. Just position yourself again at the end or start of the fight.
The achievement unlocks when you defeat the 100th enemy