What's worked for me is going into dock contents, reset it from showing running programs to not running minimized programs....then resetting it to running all. When you click on one of the Win10 system "features" (like action center) that icon likes to stay on the dock. by going back into dock settings and repeating above, it can be removed again. I know a fix to remove this issue would be nice, but that's how I'm managing it for now.

If you still experience this issue after trying what scottaco said, please contact us:

https://esupport.stardock.com/index.php?/Tickets/Submit 

This is happening to me too. To be honest, Scottaco's fix above is just a temporary solution as it keeps coming back. I also get an unlabelled icon for Windows Explorer that shows a black preview as in the screen grab below. The icon can be right clicked, but selecting Close does nothing. Selecting Remove Icon or Restarting Windows Explorer in the Task manager gets rid of it but only temporarily. I think it comes back if the PC is left idle. Background tasks in Windows 10 like to show up on the dock as running applications and this needs a fix. Current version of ObjectDock is not working properly on Win 10. Please can someone looks into this?

The invisible icons has been reported already. It's believed that due to the modern apps not having a proper .exe they don't show up properly on the dock.

For your further issues, you will need to contact us through support.

Please download and run the tool below:

http://sd.stardock.com/Support/supportToolTest/SDSupportTool.exe 

Then attach the .zip that's created and send it in with a ticket to support:

https://esupport.stardock.com/index.php?/Tickets/Submit 

Yep, it's the Metro/Modern apps, I've run into this issue myself when working on v15.7 of the Winstep Nexus dock and had to code around it. Metro apps in Windows 10 are hosted by ApplicationFrameHost.exe. The executable creates a window inside which the Metro app window itself is hosted. Even worse, the Metro window will 'stick around' even when the user has closed the Metro application itself, although no longer attached to the main ApplicationFrameHost.exe window, an issued that could cause two icons per Metro app (one of them blank) to appear in the running applications area of the dock.

Microsoft could have done a much better job of integrating Metro apps into Win32, that is for sure.

It is happening to me also and I don't have any Metro Apps on my Dock.  I only have the same apps I had when running windows 7.

I'm sure it has, but my post above shows a different problem relating to unwanted icons on the dock. It's not blank icons of modern apps running in the background, my issues is that there is a blank 'folder' type icon (see screen shot above). If you select 'remove icon' it goes away but comes back again soon after. This did not happen in Windows 8.1. 

Please submit a ticket with the requested information.

JcRabbit is correct in his post above.  It's a real problem, far beyond an invisible icon.  For me, I have a laptop with both integrated and discrete graphics.  Even when Metro apps are closed, ApplicationFrameHost.exe, as JcRabbit says, still runs.  Worse, it defaults to using my discrete GPU (Nvidia), and I can't seem to change this in the Nvidia Control Panel.  Those of you who have a similar setup might want to check if your discrete GPU is running now, because it burns through the battery a lot quicker (and wastes electricity).

One thing you could try is to disable any Metro Apps you don't want running in the background.  Windows 10 by default lets Metro apps run in the background, and you won't see them in Msconfig, Startup, or other folders.  They are managed by going to Settings --> Privacy --> Background apps.

Turning off the ones that you're not using (in my case I turned them all off) will minimize the chance of ApplicationFrameHost and it's invisible icon from showing.  If it's still showing after you disable background apps, you can terminate the process via windows task manager (although this may temporarily break the notification service / Action Center until reboot).

All that to say that while Stardock should address this issue, it can be a bigger problem than that.  MS needs to put out a fix that kills this process when there are no metro apps running.

They won't. They don't care, For them, this is not a bug.