if you combine the upgraded nail gun and any melee weapon you can easily kill the abominations in the vents which kinda defeats the purpose of them in my opinion (possible fix could to just lessen the amount of time the nail gun stuns them or remove it completely for the abominations alone).
#able to kill abominations in vents easily (probably not necessarily a bug but idk)
severe abyss
nova storm
you could also just throw a bunch of c4 at them, one of its upgrades needs you to kill one whit them as well