I've found that when notebooks go unused for some time, using them will freeze only the pop-up. It will show the cursor as if going to click on something, but no notepad. I'll experiment next time to see how exactly this happens.
There is a bug in the current version where notepads don't actually disappear when all their pages get used up, the game is trying to open the notepad UI but there aren't any pages for it to open. Simply just keep track of the amount of pages and throw out your notepads when you use up all of them.