For those still hung up on this, I say again... SIM CARD TRAY.
Every smartphone comes with instructions on how to remove and install a SIM card to their phone. It can only come out and go in one way. It's very easy to re-insert incorrectly. It's often hard to tell which way is the right way. In some cases (ala the Nexus 5; look it up!) if the SIM tray is inserted incorrectly, it will get jammed.
Some people have said, well, you don't pull out the SIM tray that often. I say, so what? There's still only one way to do it; the correct way. Some people have said, well, the consequences aren't as dire. I agree that it's scary that the consequences are worse for the Note 5, but ultimately, that's just an unfortunate circumstance.
However, none of that says it's a "design flaw" (the title of this thread) unless you can say every manufacturer has committed a design flaw in their smartphone SIM trays. Damaging your Note 5 with the S Pen can only be done if you insert it incorrectly, aka the wrong way. That sentence alone should absolve Samsung from a design flaw.
Having said that...
Could Samsung have done better?
That's a fair question. And the honest answer is, yes. Samsung could have informed the public better, too, about this.
No one -- as far as I can tell -- is arguing that Samsung shouldn't address this both on a customer service level and in the next iteration of the Note, or even as early as the next wave of Note 5's to be manufactured. Please stop this straw man. No one doesn't want this issue fixed for Note 5 owners or the future of the Note series. At least no one worth listening to anyway.
Also, please stop the whole "children or handicapped people can easily re-insert this incorrectly and so it's Samsung's fault for not addressing this" argument. Not only is this a false example, it's also a sinister use of children and handicapped people just to claim Samsung's designs are poor and/or flawed.
The bottom line to me seems to be this:
1) Samsung could have prevented this or at least been more informative about this.
2) At the same time, Note 5 users need to be aware of what can happen, and follow instructions as per Samsung's design and intent. You ought to put the stylus back correctly. Because just like many things, doing so incorrectly can lead to undesirable results.
That should be the end of the convo without needing radical examples or car engines or extreme accusations using handicapped people.
It's really time to move on.
For now, put the stylus back correctly when using a Note 5, and hopefully Samsung does better in the future.