Okay, I had the same issue myself as rwkiii – this is a bug in Visual studio and is not an easy one to fix. Here are the symptoms:
Visual Studio states that you cannot merge/switch braches/etc. because you have uncommitted changes – which is fine, except all your changes have been committed.
Cannot switch to master because there are uncommitted changes. Commit or undo your changes before you switch branches. See the Output window for details.
Here’s a screenshot to be clearer.
If you look at the output window, it may appear empty but you have to change “Show output from” to “Source Control – Git”. This will list the file that Visual Studio thinks has changes.

Now, things that I tried that didn’t fix it (so you don’t have to):
- Restarting Visual Studio
- Restarting the machine
- Switching Projects
- Using external git tools (All of which said “no changes”)
- git reset
- Making arbitrary changes to the file and committing that. Commits ok, VS still thinks there’s more changes
In the end, I had to go and delete the file from the disk, then “undo” that change from the Team Explorer window:

Not the most ideal solution, but it does seem to fix it.