This is a copy of the closed issue from 2014:
https://github.com/toggl/toggldesktop/issues/911
Please see screen recording
toggl_bug.zip
Hi I'm still not able to reproduce this. Maybe it has something to do with the dock preferences. Could you please let me know what preferences have you enabled for dock.
Also it might be issue with the speed you are closing and showing the app. Does the same happen when you wait a few seconds after hiding the app.
Hey, the time between closing and showing the app doesn't matter. If I click the minimize button, the problem will always occur.
Dock preferences are attached.
Btw.: I'm not the person who posted this issue 2 years ago. So it seems to happen on several Macs.

Bingo! If Minimize windows into application icon is enabled this bug happens. Thank you for sending the details.
Looks like that issue is fixed, can't reproduce anymore.
Most helpful comment
Bingo! If
Minimize windows into application iconis enabled this bug happens. Thank you for sending the details.