"Red is ours, Green is theirs"

"A View from the Gallery". Babylon 5 battles a horde of invading aliens moving through the sector. The maintenance guys take a break between calls and observe that when one of the Earth Alliance ships goes up, it produces a red or orange fireball, while the alien ships produce green fireballs. They attribute this to the different atmosphere mixes used by the two sides.

Example of:
Explosions in Space