Morph Ball Guardian
As soon as it takes it's form, pump missiles into it's belly. If it scratches the air twice, be warned, because it's about to shoot a wave of energy at you, which does moderate damage. If it screams, jump onto a ledge nearby to dodge the fire. Once it's in it's ball mode, you can hurt it, so use a ledge to jump over it from high above. If it hits the wall you're clinging to, you'll fall and take damage. Simply repeat the process to make it transform back into a Core-X.
This part is fairly easy. If you ran out of missiles, grab the green X floating around, then hit the Core-X with a missile whenever it isn't flashing. Dodging it shouldn't be hard. Three missiles will finish it off easy, and now you have the morph ball!
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Charge Beam Guardian
This fight is really just practice for the tougher Core-X form. All you have to do is keep from getting hit. When it is charging up to fire, it will open an "eye" - shoot it with a missile then jump away immediately to avoid the blast. A few hits will do it. Once it's dead, grab the giant X for the charge beam ability.