I observed the same behavior on a previous gen Surface Pro.
The root issue is that the Surface Pro is allowed to draw more power than the charger provides. Applications that fully load the hardware (like VMware) can cause sustained max power draw; this can cause the battery to completely drain during a regular workday even when the Surface Pro was plugged in for the entire time.
You should be able to reproduce the problem by running some other power-hungry application, like say furmark or opencl-accelerated similarity.
