When does "The reference has been modified and cannot be saved" symbol comes into picture in save scope window? Are there any specific scenario steps for reproducing & resolving this issue?

User is trying to save a 3DShape. But while saving it, 3D Shape has a red cross symbol in save scope window which means "The reference has been modified and cannot be saved", so user is unable to save his work. What might have been the reason of this issue? How to avoid/resolve this issue?