Moved to the InDesign forum.
If you are opening a file from an earlier version of ID, then the software sees it as a new file and as such the file is unsaved. It wants to Save the file in the new version.
Sometimes—and I wish I could pin down what curcumstances lead to this—but sometimes when I open a file over a network, it opens as a Read-Only doc, even though it wasn't saved as a template. I usually don't even notice this until I go to save, when it asks me if I want to replace the existing file. I expect this if I Save-As, but not when I just save. I'm not sure if this is what you are seeing too, but I wonder if you are working locally, or over a network?
This can be caused by many things, ownership of the networked drive, properties of the file ie: ready only.
When opening a file over a network the path to linked files will alter to your machine and indesign will want to save the file again even thou you have not made any changes.
Would be good to know if you are on a mac or pc network.