When a Fission Metroid splits, pay attention to what color they take to know how to kill it. They will randomly take on a vulnerability to one of your Beam weapons, determined by its color. Switch to the correct Beam to destroy it.
Yellow = Power Beam
Purple = Wave Beam
Light Blue = Ice Beam
Red = Plasma Beam
Note that Fission Metroids can also be defeated with Power Bombs, which is particularly useful when there are many around you at once.