Why are unmodified prefabs unaccountably saved?

I know by default Ctrl+S is used to save file that has been modified.That's why I am here to ask a question.

My team got used to use SVN for version control,when we modify the prefabs and use Ctrl+S to save the scene,then SVN commit the changes,We always find some unmodified prefabs are modified too(Those files are in SVN Commit File List).But we never modify those prefabs.It troubles us a lot.

By the way,I did an experiment.In PlayMode,I change the active state of a prefab by the window of Inspector,then quit PlayMode,use Ctrl+S to save.I find the prefab is modified since it can be find in the SVN Commit File List when I use SVN_Commit.

When I use BeyondCompare to verify what happened to the prefab,I found it is really modified,I don't know what exactly happened.