Yet another bug has been reported in conjunction with Windows 10 1809, this one just recently. The bug seems to have existed since Windows 10 1809 itself has existed, but Surface customers are now just finding it.
Windows 10 1809 can keep track of battery levels for Microsoft accessories with an add-on app. But, with the latest update, the app has stopped checking the Surface Pen battery.
In the example above, the Surface app shows the pen at 99% battery, yet in Windows 10 Settings the battery level shows 94%.
So, Windows 10 1809 itself tracks battery levels just fine, but the app no longer does. Microsoft will most likely need to update its own Surface app to work correctly with Windows 10 1809. The workaround, of course, is to use Windows 10 1809’s battery tracking for now.