This caused me a lot of grief before I realized what was going on and is now forcing me to power the project with the uno while running it on the yun.
The ability to offload WiFi to Linux on the card is great. You can sinoke call the Linux process and return the results. I used curl.
yun volts measured

Uno volts measured

I bought a second one to check and it has the same freaking problem. 4.68-4.71v coming out the 5v pin. No other arduino uno or mega has this issue.