There was an uproar when note 5 launched which caused the phone to get permanently damaged if you inserted the s-pen the wrong way and tried to pull it by force. When contacted, Samsung suggested that the s-pen is intended to be stored in a particular way in the handset and user should read the manual properly before using the note 5.
The initial shipments must have been sold and Samsung had manufactured the note 5 in second phase. This time around, the note 5 comes with a warning that tells you to insert the s-pen in the correct way. And the s-pen stylus slot flaw is something that user have to live with the entire life time of the device.
The instructions specifically say that the s-pen was designed to be stored in the devices with the tip first going into the device and not the handle first. When inserted the wrong way, the handle holds onto the latch and when you force pull it, the latch will permanently get damage. This will cause the note 5 to lose the ability to distinguish whether the s-pen is inserted or removed into the handset.
When the handset loses this ability, it won’t be able to launch the s-pen option that you usually see when you pull out the s-pen thus making the note 5 lose much of its s-pen values which distinguished in a sea of android galaxy devices.
Fortunately, even if you inserted the stylus in the wrong way, there is a work around to get the stylus out. Check out the below video that guides you in getting the s-pen stylus out if inserted in the wrong way.