If I had to guess, you are running Windows 10. I believe this is caused by interacting with the taskbar thumbnails. Stardock tech support have not been able to reproduce this issue.
Here's how you can test this:
Open Groupy2 and on the General tab, set "How should taskbar buttons for Grouped windows appear?" to "Show all." Now open two or three windows in one group and then hover over the the taskbar button for the group and click on one of the taskbar thumbnails and then try to move the grouped window. Try again after clicking on a different taskbar thumbnail. See if you can reproduce the issue you are having.
Here is a link to a video I created to show this issue.
https://1drv.ms/v/s!AlPnZU3br_UOh-Fs3EZihLCxYT_CJA?e=qsuRUC
Note how one of the windows moves without the Groupy2 bar.
