I would like to submit two examples of immune systems functioning in some sense too well and therefore crippling people.
Asthma and allergies
I have asthma. This means that my immune system responds to certain airborne stimuli by saying “you know what will really help this situation? If we Stop Breathing in those bad things. Let’s contract your air tubes in there to limit the airflow and the bad stuff.” Those stimuli could be as benign as, I go for a jog on a dry-air day and the ‘bad thing’ is a lack of moisture in the air.
I have several allergies too, in particular to the droppings of dust mites and certain particles of hay dust. This means that those things are, as far as anyone knows, benign and not trying to harm me—but my immune system recognizes them as Dangerous Invaders. Maybe they are, maybe they secretly tear up cells and stuff but nobody ever gets exposed to enough of them to do lasting damage. Either way.
The combination is really really bad. I breathe in too much dust and then it gets trapped in the mucous in my lungs where it causes a sort of pneumonia—fluid and mucous buildup in the spongy matter of the lungs which then has to be coughed out through those same air-tubes. But I cannot cough very well because my air tubes are constricted! To solve this I need a rescue inhaler which contains a compound called salbutamol, which happens to relax my air tubes so that I can spend a day or two coughing out all of the bad stuff and return to normal life.
But if I couldn’t, then life would be really difficult. Not being able to breathe very effectively because you are breathing through a straw makes your brain panic and becomes like the only thing you are able to focus on.
And it doesn’t come from my immune system being too bad but from being too good. Like it’s trying to crush enemies that most people don't even bother trying to crush because the damage is so low—but it does not tolerate even the least bit of attack and goes out to tear some shit up.
Foreign body giant cell reactions
One of the worst biomedical engineering disasters ever concerned a prosthetic tempromandibular joint (TMJ) replacement.
I know, I know, “ah yes... the tempromandibular joint!” Let me give a digression to explain. Your lower jaw, the mandible, moves in ways that like none of your other bones move. It does not just swing open and closed like a hinge (your knee, your fingers) and it also does not just rotate around in a circle (your arms, your legs) but some hybrid of the two. You can probably put your lower teeth over your upper lip by jutting your mandible outward or put your lower lip under your upper teeth by sliding the opposite way, in addition to the normal hinge motion. You can also slide your lower teeth left-to-right. You need these motions in order to chew food effectively.
To do that, the bones are different. If you make a fist and then wrap your other hand around your fist, this is how most ball joints work, there is a "socket" and a "ball" inside of it, the socket keeps the ball in one place.. The bones are covered with a smooth barrier called cartilage and the body lubricates the joint with interstitial fluid and that is how it rotates—slide your fist around in your hand. But for the jaw, it is like if you make two fists and place them next to each other. To keep them together, you need an additional disc of cartilage that looks like a concave lens, it is hollow on both sides to form a little socket for both balls, but it otherwise lets the two balls slide around on each other without falling too far one way or the other.
Long story short, some people lose these pads of cartilage and then they have to have it replaced with a hinge and then they can’t chew. So some biomedical engineer had a great idea to create a plastic bag containing a gel that mimicked the original pad of cartilage. Unfortunately he verified that the bag could withstand the forces required on a model that was some scale factor larger—let’s say for this answer that it was like a factor of 10 or so. (It’s a small pad of cartilage!) He had this very very comfortable safety factor, but he was apparently blithely oblivious to the fact that materials fail due to stresses, not forces, and when you scale down by 10x, the same force causes 100x the amount of stress. So what seemed to be “really safe” was actually “under really dangerous amounts of load.” The bags broke, and released their gel contents into the body.
That also didn’t seem on-paper like it would be too bad. The gel was made out of little grains of plastic called PTFE, trade name “Teflon”. This is used all the time in all sorts of biomedical equipment. It’s super slippery and chemically really inert because it has these fluorine atoms holding on so strongly to these carbon atoms that they cannot be kicked off and they don’t want to grab onto anything else. So it is a great way to slide a biomedical implement into something, slide it back out, and minimally damage the surrounding tissue.
So it’s a safe material and everybody made it out all right, right? Nobody lost half their face due to this thing and the story can end here?
Well, the folks’ immune systems in many cases thought those little grains were like splinters—what the doctors would call a “foreign body”. When the body sees a splinter it combines white blood cells into massive weapons of devastation called “foreign body giant cells” which exist to dissolve that splinter completely. They do a lot of collateral damage while they do so. But they press in and blast the splinter with acid and dissolve it and then the bloodstream takes the bits away and eventually you pee out the now-atomized splinter bits, as well as any other of your cells that were nearby.
At least, you do that, if the splinters are not super-slippery chemically-inert plastic and just slide into other tissues in the body when something pushes against them. If that happens, then the foreign body giant cells just chase the splinters around your body forever destroying all of your own cells in the process. It's really really bad. It's basically having an allergy-on-steroids to something that you cannot get rid of which has invaded your body.
So uh yeah. The immune system is doing really really well, it has just been handed a deeply unnatural task that it cannot possibly be prepared for.