I am having the same issue. I noticed it today when I played a bit with the Microsoft Remote Desktop in the landscape mode. The X button to close a window is at the exact spot. I was I bit annoyed that I couldn't close a window with the s-pen, but I could with a finger. So I checked in the test menu and I saw the problem there.
I was thinking of returning the phone as I also have the multi-touch problems experienced by multiple users of this forum. I will probably contact the Samsung support to check what they have to say about those issues. I really like the phone and those might be minor issues, but they can be quite annoying if you have an expensive phone like Note 3. I will check in the local shops if the phones there also have the issues.
EDIT: I have attached an image of the s-pen test menu. Don't mind the pink tint, as I used a crappy phone camera. You can see that the s-pen isn't detected in the lower right area. In my case, there here is also a small area in the lower left corner.
EDIT 2: I have spoken with Samsung support. They have told me that the inability to use this area with the s-pen is due to a design constraint. I have also asked about the multi-touch problems and they have told me that it is not intended to use more than two fingers.
Greetings and have a nice day.