Sometimes I move between branches which have a submodule pointer pointing to different submodule commit. I am not sure why this happens but after checking out the other branch, this pointer stays the same and is marked as a staged uncommited change.
In the terminal I would reset the branch, but in SM I see discard changes. Clicking on it makes the changes disappear from SM UI for couple of seconds and the they reappear. Looks like a bug to me.
Update: here is a description of the situation I have: https://stackoverflow.com/questions/40219209/does-git-submodule-branch-switch-along-with-main-projects-branch