You surely committed or stashed more than once in your lifetime without previously saving everything in Visual Studio. Are you using Panic Save* ever since? At least, this happened to me and my team a couple of times. This extension saves all changes when you leave your current Visual Studio instance, e.g. when you switch to GitExtensions window for committing, stashing and pushing.
* Panic Save is the behavior when the user presses Ctrl+Shift+S repeatedly in a short amount of time, before switching to the GitExtensions (or any other) window.
Please go to the github repository to file issues and start discussions.