In the past when cropping a photo, I've often created a duplicate layer and done the cropping on that - so that the base image remains unaffected.
Today, however, when doing that, I realized that the cropping was affecting the duplicate layer as well as the image in the layer underneath it. One possible reason might be that I had merged visible layers before creating the duplicate layer. Might that be the reason? Thankfully I was working on a separate "test" version of the file so the original file remains untouched.