To easily defeat the rock miniboss on Jewel Man's stage, equip the Hornet Chaser. The Hornet Chaser, when deployed, will attack and damage the rock foe even when he's on the ceiling, forcing him to come down where you can quickly finish him off.

To easily defeat the flame dragon miniboss on Magma Man's stage and in Dr. Wily's castle, consider equipping the Concrete Shot. Five shots to the face of the dragon with the Concrete Shot will quickly dispatch it. While the Black Hole Bomb will suck all of the flames off of the dragon's body, rendering it unable to attack, it won't heavily damage the dragon itself. Use the Concrete Shot instead.