Yes, I ran into the same issue after the update and I was able to find a workaround.
If you are using iOS, activate Siri, then close out of it. Your audio levels will be back to normal afterwards.
Here is another workaround, in case the previous one doesn’t work.
I’m not sure if this works for everyone (and it’s not really a solution), but when I skip to the next track the volume goes back to normal. If I switch apps and reopen Pokemon it lowers the volume until I skip tracks again, but otherwise it stays fixed. I’m on iPhone with iOS 10.
It appears that there is a potential workaround for Android users as well. See this post:
Music is stopped each time you launch/reopen the game on Android. If your music player supports quick controls in the notification bar (e.g. Google Play, Amazon, Pandora), it can be restarted there. If they don’t have a Play/Resume button there, it seems you’re out of luck.
Additionally, it looks like this step may or may not be required:
you have to enable notifications for whatever music player you’re using and then you can play it from the notification screen