This issue will be faced by almost everyone who has implemented the Cross Site Publishing in SharePoint 2013. Let me again explain the Problem statement once again, so that it will be a bit clear. (I know, the title is not clear J)
Let us assume the following scenario.
1. I have a page layout
2. Have created some pages based on the page layout
3. Using the Term Based Navigation and the terms are pointing to different pages which we created just now.
4. E.g., The Term1 – Navigation Page would be Page1.aspx which is created based on the PageLayout1
5. The Term2 – Navigation Page would be Page2.aspx which is created based on the PageLayout1. (The same layout which the Page1.aspx is using)
6. Now, when the User comes and Edit the Page1.aspx, SharePoint will be asking for an Option, either you want to edit the Page1.aspx as an individual URL or you want to Edit the PageLayout itself.
7. In one of the environment which I was working, this popup was not coming.
8. Then I found that SharePoint is clever enough to display this warning message, if there is one or more terms using the same page and one or more pages has been created based on this layout. If there is only one page created with this Layout, then there is no need of asking this confirmation.
9. Though this looks very simple, I spent some considerable amount of time to understand this and the intelligence of SharePoint. Thought of sharing this to the community as well.