How to keep PWM from "contaminating" analog read values on my pcb
As mentioned in other comments/answers, the definition of the needed S/N-ratio is missing.
Some users - like broadcast studios in Europe - demand 114dB or more.
It is not only about the possible Audio coupling, but any HF-interference is also critical. F.e., many users have problems to listen to weak radio stations at home when a nearby LED lamp (without enough built-in HF filtering electronic) is on, since some of those bulbs are using PWM resp. step functions in their power supplies. 

Even when listening to a weak FM sender in the 100 MHz range the receiver can be flooded with noise, though the power supplies have working frequencies mostly in the 25-120kHz, way below 1 MHz. 
A LED light bulb needs more power then a LED for a switch illumination, but there might be still a problem. 

To overcome these issues, it is always better to avoid PWM where possible in this case.
With a few hundred mA of current, an option is to use non-switching series regulators. The difference is only a little bit higher energy consumption and maybe a bigger heat sink.

Some 40 years ago, there were some HiFi- FM-receiver designs with multiplexed 7 segment LED- displays. To reduce the noise, those LEDs were fed by integer numbers of rectified sine waves instead of direct current.

It was a complicated design with much shielding metal inside and this is the reason why they switched to LCDs with it's much lower current, so producing much less noise.