apps won't properly quit or force quit

i've been having a strange problem on my macbook pro (el capitan 10.11.5, 2.5 GHz processor, 16 GB memory, everything completely up to date) where certain apps won't quit properly? like i’ll press ‘quit’ and everything will act like it’s quit, and the application doesn’t show in activity monitor, but it still appears in the dock with the little dot under it that means it’s still running, and it appears in the force quit panel as well. when i right click the app in the dock, the force quit option appears but attempting to force quit does nothing. the “killall Dock” command in terminal does nothing. when this happens, i can’t even shut down or restart my computer (again, clicking either option does literally nothing) so i have to shut it down by holding the power button. only when i restart the computer that way does the app seem to be properly closed.

i’m not sure what determines which apps do this - so far it’s happened with adobe media encoder, the sims 4 / origin (opening the sims 4 opens origin, and then neither will properly quit), stardew valley (which i run through wine, because it’s only for pc and i use a macbook), pixelmator, illustrator, and photoshop. i thought maybe it was a problem with my old laptop because it couldn’t handle the processing power certain apps take (these are all apps that would suck up my old laptop’s battery life like a vacuum, even while plugged in, i'm talking at least one percent per minute), but the issue has followed me to my new laptop (i used time machine to transfer everything from my old computer to my new one) so i guess it’s a software issue? but it only started maybe a week or two ago, and i don't know what i could have done to cause it. anybody have any ideas? google hasn’t been able to help me, all i see is “go to activity monitor and find the app and force quit from there” which is useless, because they don’t show up in activity monitor.

MacBook Pro with Retina display, OS X El Capitan (10.11.5)
Has invited:

howapple - hello

Favor from:

As a Test I would recommend uninstalling all Wacom software.

And verify there are no remaining Wacom items in your log-in items.

>System Preferences>Accounts>Log-in Items. Use the to delete, unlock the padlock.

Restart and test.

If Wacom is mission critical to your work flow, then try reinstalling latest updated Wacom drivers/software.

It is a known issue with 10.11.5

To reply to a question, please Login or registered