I can replicate it like this:

1. Go to Activities
2. Select an application that needs root (Synaptic, GParted, etc)
3. Press enter to launch and hold it until the root authentication dialog pops up
4. I can start to enter a password (optional)
5. After a few seconds the screen will tell me "that didn't work" and disappear.

This doesn't happen when:
- I use my mouse to start the application from Activities
- I tap enter really quickly, letting go before the dialog pops up (quite hard to accomplish if my computer responds quickly)

It seems the dialog interprets the "enter" press that originates in the Activities view as well. Imho the best solution would be to not allow the dialog to check an empty password (assuming it doesn't pop up on accounts with empty passwords), or to make sure it listens for the act of pressing enter, not having enter pressed.