What level is each spell? Level can make a huge difference.

Skill level.

And if you want to boost fire damage, use a Magic Knight (+25% elemental damage, or +50% with 25 lovers) with +50% fire affinity (and/or use Firefighter innocents to boost it to +99%). Those multipliers on elemental damage is why staff-wielding Magic Knights are the best units in the game.

Elemental Affinity

https://disgaea.fandom.com/wiki/Elemental_Affinity

Originally posted by RafaelSO:

Elemental Affinity

That doesn't explain why Mega Fire would do more damage than Omega Fire

Mega hitting for more than Omega, assuming no other changes between uses(like targeting), would require that Mega has a notable skill level advantage compared to Omega. Skill levels apply a power boost, so something like a Lv2 Omega Fire vs a Lv40 Mega Fire could easily favor Mega.

Next, you have to be certain that it's not 2 different enemies being attacked. If they are, they could have varied equipment(and thus Res stat) and varied Fire affinity, which could add enough variance to make Omega weaker than Mega.