Samsung responds to the Note 5 S Pen flaw:
“We highly recommend our Galaxy Note5 users follow the instructions in the user guide to ensure they don't experience such an unexpected scenario caused by reinserting the S Pen in the other way around”
The Korea company's response is rather similar how Steven Jobs responds to Antennagate "Just avoid holding it in that way.", the iPhone 4 signal issues.
Anyway, it shouldn't be a problem once the owner have used to the usage of the Galaxy Note 5. But always do keep in mind - avoid inserting it the wrong way.