Hi,
If dragging a note makes the generator to create a new dungeon, then I guess you're using it on a phone or tablet, it it right? Touch UI is seriously messed up here (even more than in my other generators). There are ways to make it work, but overall this generator is not designed to be used on mobiles. In the next update a few touch-related bugs will be fixed. I don't know when this update will happen though.
Meanwhile this is what you can do:
- Try automatic rearranging of the notes (Notes > Rearrange notes), maybe the generator will find a better layout.
- Try disabling the Zoom-to-fiit and Rotate-to-fit options. The screen space will be used less efficiently leaving more space for notes.