Despite being the default controller of the Nintendo Switch, the Joy-Con can be quite the temperamental piece of equipment, especially its thumbstick. Its infamous drift is the most well-known problem of the controller but is far from being the only one. Another issue that some people have is that cap on the Control Stick is so fragile that it can bend or come off after a few hits.
After playing long hours with your Joy-Cons, you might find that the caps on your thumbstick start getting bumps, the plastic begins to peel and the whole thing might start to feel a little loose and eventually fall off.
Why does this happen?
The reason why it happens it´s obvious. Wear, tear, and time. Hitting or scraping your Joy-Con is the main reason why damage appears. Applying too much pressure while tilting or scratching the stick in frustration are also prime reasons for the plastic to bend (as well as not being careful when you clean it). This can happen to every thumbstick regardless of the controller, be it a Joy-Con, Pro Controller, or even a Dualshock..
The real question is if it happens more often on a Joy-Con than in other gamepads. The answer seems to be yes, although not by much if the market for replacement caps on Sony´s and Microsoft's controllers is any indication. In any case, the plastic cap of the Joy-Con´s stick is notoriously flimsy and can be bent without using much force, so it can be a bigger issue for the Switch.
Joy-Cons are not a particularly resistant piece of equipment. "Light" hits or extended hours of play can take their toll on the cap and wear it down.
How can I prevent this?
By being careful with your Joy-Con. Don´t hit it, scrape it, or let it incur any physical harm. The Joy-con is fragile like a baby, and you wouldn´t let a baby fall to the floor, right?
Aside from those general directions, try to not exert too much pressure on the stick. You don´t need to apply the full force of your thumb to tilt it forward. Doing so can be quite taxing on the caps, and your muscles as well.
But if you reading his article, then your Control Stick is probably already damaged, so your real question is...
How do I fix the cap of my thumbstick?
If you only have bumps or "deformities", then you might want to try and wait overnight to see if they smooth themselves over with time. If you have googled this same question and arrived on this article, however, then you probably already waited a long time and nothing happened, so let´s try other fixes.
To fix your cap, you can try massaging the bumps back into place, trying to rub the peeled plastic into its original shape. This will take you a while and might seem futile, but remember that the plastic is quite soft, so soft that it can be bent with your fingers. Continually push the plastic into the holes they popped out from until the problem is fixed.
If the damage is beyond mere bumps and the cap has fallen off completely, then don´t go buying a replacement yet. You might want to try just placing the cap back on the stick like nothing happened. If the plastic is still in good condition, it should be able to hang on again without doing anything else, albeit it will now be a bit looser.
If that doesn´t work, there´s the tried and true tactic of putting glue on the cap and placing it back again. Of course, this can backfire if you half glue the cap back on, leaving you with a very loose thumbstick that doesn´t fit right under your finger, so be careful with the glue.
Of course, before you try any of this, it´s a good idea to contact Nintendo support and see if they can do anything for your Joy-Con. They might be able to help repair it for you.
If they can´t and the problem persists, then...
Time to replace the Joystick
This isn´t as costly as it might seem, caps are pretty much the cheapest Switch accessory after a screen protector. There are hundreds of alternatives all over the web, on eBay, Amazon, and other sites. In fact, it´s common to replace the stick on other controllers to replace them with a taller nub in order to increase precision.
If only the cap is gone, then you can buy one of these little replacements and just slap it on top of your thumbstick. If the damage is worse and you can´t just slap a plastic cap on top of the problem, you will need a more advanced kit to replace the joystick in its entirety.
This is a good kit to start with, as it has all the parts and tools you will need to replace the whole joystick. How can you replace the joystick? Fixit has a pretty good guide on it.
I could give you the cliff notes, but honestly, the process is complicated and you can accidentally damage your Joy-Con if you do it wrong, so it´s best to stick to the original guide and its step-by-step pictures. If you don´t think you can do it, then it´s best to throw in the towel and call a professional, else you´ll be buying a new replacement Joy-Con anyway.
Regardless of if you put on a new cap or replaced the whole joystick, you must calibrate the control sticks when you are done to make sure they work right. You can do this by going to the Systems Settings and choosing the option from the Controllers and Sensors menu.
And that´s it, hopefully, you have been able to fix your issue, if not then you might have no other choice but to buy an additional Joy-Con.