Of course it's a flaw, and it's a pretty glaring failure point. If the joycons jam when they're put on the wrong way around, guess what? *They shouldn't slide on that way*, it's pretty obvious. It takes no effort at all to make a one-way rail *actually work one-way only*, it's a matter of adding a single peg on the end of the rail or using two different heights of the lip on each side, but Nintendo didn't even do that. If you see potential for error, as a designer it's your job to eliminate it - you always operate under the assumption that the unit will be used by the biggest dimwit in the universe, and it probably will be. There's a reason why polarised plugs are protected from being inserted the wrong way around - because plugging them in the wrong way will damage the device and no amount of markings can change that. There's a reason why PC components are on keyed cards - because there's always someone who'll try to put them in the wrong way around and it's your job to stop that from happening. This is the engineering equivalent of implementing a big red button that breaks the system and telling the user not to press it. At that point it doesn't matter whose fault it is if the button is pressed, the button shouldn't be there in the first place.
Or y'know, they shouldn't slide in the wrong way at all, because there's no reason why a console should feature a trap for users who don't pay attention. Defending obvious design flaws is completely beyond me, this is simple stuff, I don't know why Xzi disagrees when it's a pretty general consensus. If it wasn't an issue, there wouldn't be instructional videos showing how to loosen them with a flathead screwdriver online.