Once in a while Groupy has some problems with setting the focus of the current application window. This may sound a little bit vague, but that's because it is.
But I have found one situation which seems reproducable, on two separate (Windows 10) computers, which may help pinpoint the issue.
- Set notepad.exe to automatically group.
- Start the command prompt and execute notepad.exe. It will focus Notepad.
- Return to the command prompt and execute notepad.exe again.

In my situation it will start Notepad, but immediately returns the window focus to the command prompt. The keyboard focus however will be still in Notepad. You can click in the Notepad window, but the command prompt will stay on top, until you click on the Notepad icon in the taskbar.

This also happens when launching Notepad from a PowerShell window.