What are your video game enemies that are worse than the final boss.

Runebears in Elden Ring, by far. The one in Caelid still kicks my ass even after I beat the Elden Ring with my hands tied behind my back.

The Bell Bearing Hunters are also brutal, both the Leyndell and Caelid ones only die due to cheese, but I didn't cound them since they feel more like mini-bosses than the runebears do.

the souls dogs are always annoying, except for Bloodborne where they decided that they wouldn't be an issue anymore and instead created the abhorrent creatures know as the brainsuckers

Dead Space. 3 tentacle shooting small creeping "baby" guys. I know that they are somewhat easy to kill but they always make me panic. From the Souls series, contraptions and of course the dogs.

Loxes in Valheim. It feels like they have infinite hitpoints.

Muckroaches, Stilkins, and Spit Squits in Silksong. Muckroaches move erratically, and you can never really tell when it's safe to attack and when they're about to lunge. Stilkins spend most of their time underwater, making them hard to hit, and their projectiles are difficult to dodge in the cramped environment they're in. Spit squits almost always dodge whenever you swing at them, but thankfully you can trick them into getting eaten by barnacks or flying into traps.

Speaking of tentacles, here's another one: Half-Life blast pit monster
It was annoying because it was listening for sound (steps, jumping). Once it heard like a single step, it could hit very close to you, repeatedly. Sometimes it hit and killed you.
The final boss on the other hand (the Nihilanth) is easy to dodge. Just hide behind pillars if memory serves.

The first thing that came to mind were Cazadors from fallout new vegas. I haven't even played the game in over a decade and I still remember the name. I think they were just too powerful, yet too easy to stumble on early in the game.

Potentially any random encounter in SMT3