I was very happy to find the instructions for USB WiFi config. This is a great feature.
This page
suggested I put my Photon 2 into DFU mode. However, when I did that and clicked the button "Device is Blinking Yellow", it then said something like "this won't work when your device is in DFU mode, put it into Safe mode".
That didn't happen when I tried it; it just went to configure Wi-Fi and did not change the device mode.
Since the USB Wi-Fi setup tool uses the same code as web device doctor and device restore USB it appears that some condition is causing it to go down the flash and set up device case, which requires DFU, for you.
It's a bug, but I don't know the cause or have a workaround yet.
Which device and Device OS version were you trying to configure? And what mode was it in (listening mode blinking dark blue, normal operating mode, blinking green, etc.)?