Unrelated changes in scene text file

I'm noticing lots of unrelated changes happen on a small change in the text file of my scene.

For example, if I change the position of a rock, for some reason, lots of other unrelated objects(trees, characters etc) will have some of their values change in the text file of the scene. This is being a huge problem for doing any version control for us.

Does anyone know why this would happen and what would be the remedy?