Not seeing all files when browsing stash

In an Xcode project I have a script which adds a bunch of unstaged configuration files that are not to ever be staged or committed, but just for building and running with different configurations. I made changes to other files and had to stash and I stashed both the configuration files and the files I made changes to. When browsing the stash later the stash only showed the configuration files and not the files I made changes to. Obviously, I thought I had made a mistake when I stashed and started to recreate my changes... later I decide to try and apply the previous stash and the files that I had made changes to were actually in the stash, just not visible when browsing the stash.