Touch Bar no longer controls iTunes
The first thing I would do is reset your NVRAM.

Resetting the NVRAM on Late-2016 MacBook Pro models

Older Macs had what's called Parameter RAM (PRAM), newer Macs use Non-Volatile Random-Access Memory (NVRAM). To reset the NVRAM on all Late-2016 MacBook Pro models (with and without Touch Bar) follow these steps:


Shut down your machine. Yes, a full shut down, not just logging out.
Press the power button and then immediately press the commandoptionpr keys. 
Keep these keys pressed down for at least 20 seconds!
Let go of the keys and let your Mac reboot normally.


Note: When you log back in you may need to readjust some of your system preferences (e.g. speaker volume, screen resolution, startup disk selection, time zone information, etc).

If resetting the NVRAM doesn't resolve it, try resetting your SMC as well. 

Resetting the SMC


Shut down your Mac
Unplug the power cable from your Mac
For 10 seconds, press and hold at the same time the shiftcontroloption keys (on the left side of the built-in keyboard) and the power button
After 10 seconds let go of all keys and the power button 
Plug in the power cable
Turn your Mac back on with the power button.


Let me know how you go, as there are other things you can try. However, I've found that resetting the NVRAM and also the SMC will usually resolve unusual or random issues pertaining to the Touch Bar.

--[EDIT]--

This edit adds further things to try in order to resolve this issue. However, since macOS 10.12.5 has just been released, I would update the OS prior to trying the following solutions.

Use Terminal to kill the Control Strip

This is a straightforward way to manually reset the Control Strip. To do this:


Launch the Terminal app (by default located within the Utilities folder)
Enter the following command killall ControlStrip (or you can just copy and paste it in)
Press return


There is no need to restart the Mac after doing this.

Change what the Touch Bar shows

In System Preferences you can change what the Touch Bar shows. I would change this, exit System Preferences, and then change it again (if necessary).

To do this:


Got to Apple > System Preferences
Click on the Keyboard preference pane
Ensure the Keyboard tab is selected
Around the centre of the screen you'll see a Touch Bar shows drop-down list
Change the selection to Expanded Control Strip (if this is already selected, change it to App Controls with Control Strip)
Exit System Preferences
Test your Touch Bar music controls
If it doesn't work, repeat steps 1 to 5 and change the Touch Bar shows drop-down list selection back to the original selection and test again


Troubleshooting steps

If all else fails, you can try these troubleshooting steps:


Function keys - Press the fn key and try using the F7, F8, and F9 keys respectively as your media control keys and see what happens.
Use another user account - Try using another user account temporarily to determine if the problem persists. If you don't have another user account, you can add one in System Preferences > Users &amp; Groups. Once you've added it, log into it and see how your media controls work.
Safe Mode - Boot your MBP up in Safe Mode and try using the media controls keys. To do this, hold the shift key down as you boot up. This will take a little longer to boot as your Mac cleans caches, runs some diagnostics, etc. Once you've tested, exit Safe Mode by restarting your MBP and then test your media control keys again.


Once you've tried these troubleshooting steps, report back on what you found.