There can be a couple of reasons why a "?" shows up in the Application row. 

It can be due to an application having been uninstalled. Or you updated an application and created a new version and folder and removed the older version. These will both create a "?". 

The image to the right shows the Pen Tablet panel. This can also be the Quick Keys panel.

[1] It shows the "?" that appears once you uninstalled an application or an updated application and the old version was removed. 

[1] To remove the "?" from the application row, click on the "?" icon. You will notice the Yellow bar appears under the icon.

[2] Click on the Gear icon and select from the dropdown menu Remove Selected Applications. 

Click on the Remove button, which will then be removed from the Application row. 

[4] The icon has been removed.