I forgot to say I have a Nook HD+
Issues with Shelves are, unfortunately, quite common.
They do happen with B&N books too - However, they seem to be most frequent when either
1) You have a SD card.
2) You have sideloaded books on an SD Card.
IN V2.0.5 B&N has added some fixes. However, a few people still get issues.
First thing to try would be to update to V2.0.5.
Go to Settings.
Then Device Information
On right will be your software version number.
If it doesn't say V2.0.5 then tap on it and you'll get a green 'Check for updates' button. Tap that to update.