At Mariposa, they weren't send to kill any super-mutants, there were there to use Redding miners as slave to help them extract FEV, and the miners became so much exposed to it that they turned into super-mutants. Some thought they would need to kill them after they got the sample, but the situation went out of control. The newly turned super-mutants managed to inflict large casualties to the Enclave troopers stationed there, who only managed to seal the entrance, instead of actually kill their opponent. And it is even unclear if they managed to kill any super-mutants. The logs telll that when they shot one, not only two more were coming, but the first one also waked up. They were beaten by people who were just turned into super-mutants, not well organized, and who weren't prime humans to begin with.
Also, the Enclave did send Horrigan there. Although he was just a regular trooper. The Mariposa event made him a super-mutant, and sealed his fate.
About the gameplay version of super-mutant there are many differences with Enclave :
- The SM don't have any kind of armor. Even if their skin is thick, their resistance is nowhere near as power armor.
- The SM have mostly area weapon and use them regardless who is in the area. They keep killing each other when firing at you.
- The SM have limited weaponry. Mostly big guns and a few laser. The Enclave have much more varied weaponry and get the new gear from Fallout 2.
- Amongs their weapons, the Enclave have some ammos specifically made to penetrate armors. Which means that your power armor effectiveness is significantly reduced. (you can also use that stuff agains't them)
- The nightkin truly have a deadly potential, except that they aren't really invisible ingame, which makes much less effective as they are supposed to be lore-wise.
Anyway, the point is that the gameplay doesn't always reflect what is established in lore. Beth tends to do worse, but the previous titles aren't free of that issue.