With previous versions of the Note, it was difficult to insert the pen incorrectly. It required a certain amount of force, making users aware that the pen was facing the wrong direction. With the new Galaxy Note 5, inserting the pen incorrectly requires virtually no force, providing users with no warning that they are mistakenly reinserting the pen backwards.
Removing the pen from its slot is supposed to launch either a quick note taking app or the S Pen's radial menu, but a video from Android Police shows that this flaw with the S Pen slot could permanently disable these features. However, a similar article from Ars Technica reported that it was able to get the features working again.