Interesting... I just looked at one of my Yuns and the headers are indeed marked the same as an Uno. But the Yun is much more like a Leonardo (which shares the 32U4 processor) than an Uno (which has a 328P processor.)
Note the labeling on the Leonardo:
My guess? With all of the extra Linux and networking stuff on the Yun, they didn't have room to put silkscreen on the board like on the Leonardo. So instead, they used the silkscreened headers from an Uno, even though there are a few differences? At least the pin numbers are right. ;)
D13 is connected to processor pin PC7, which has a few alternate functions, one of which is timer 4 output compare A. So it most definitely can do PWM.
9- is wrongly marked too.
I'm sorry, I neglected to include pin 9 in my previous list. D9 is processor pin PB5. which can also be timer 1 output compare B, or timer 4 output compare B. So it also can do PWM, with a choice of two different timers.
It also looks like D12 can technically output PWM, but it appears to be strictly the inverse of the PWM on pin D6, so it's not all that useful. Probably why they didn't bother to indicate it as such.