Could it be:
I am one of your greatest enemies, I tear you apart and leave you like a shell.
Harmful bacterial diseases make you sick, and kill living tissue.
Now I end you, one of my specialities; torture and debase you, similar to hell.
People can die of nasty diseases ("end you"), and even if they don't, it can feel like hell.
So tremble in fear against my might, I am the stuff of nightmares.
As per above
I am an endless decay, a blight, here to expose your affairs.
Biological decay is caused by bacteria. Ultimately, flesh rots and the inside of a body is exposed.
Desperate, you'll try to kill me, only for you to succumb to me.
We take antibiotics to help the body fight/kill the bacteria.
Evil incarnate, you're forced to see, I'll ignore all your pleas.
But some infections ignore treatment.
In your childhood, you feared me, as an adult, you recognized me in others.
Children fear getting sick. Adults recognise others when they are sick.
If you see me, you shall flea; I'll tear and break down this world with my brothers.
(I presume "flea" should be "flee" - otherwise this is an entirely different ballgame.) People do their best to avoid harmful bacteria when they're aware of its presence. Ultimately, all living things get consumed ("tear down this world") by bacteria (who exist in their countless trillions ["brothers"]).