That's going to happen man. Another friend of mine was using his Note 3 with the S-View wallet case that he bought along with the device.
The alignment was perfect for the first few days (if there was any, he probably did not notice). Then from the third day on, the right side of the screen became somewhat unresponsive. Tried it out myself. The digitizer was being recognized but in the wrong places altogether.
He started using some TPU case from Spigen I think and the problem vanished in a jiffy. Try that out. It's not a problem with your device.