Some Applications stay in Dock after closing After i cloes the Applications the Instances still be shown and can't be force closed.

Same with the Dock only if I kill my Dock in my Terminal it reduces the symbol to 1. 

Also the processes don't show up in my activity monitor.

Would be great if anyone could help me!
I don't think it' malware. I have the same problem after installing 10.11.5. 
I found a (not so nice) workaround: 

When the app is still running: Save all changes and force quit the Application

When already quit the app: Open the Activity Monitor and force quit the Widowserver Process. You'll be logged out. Now restart the mac (don't just log in again) and you can use it without having the icons in the dock. 

I think it's an 10.11.5 issue.