tmatsoukas wrote:
• This happens frequently for me on Safari (but I have also seen in it in mail.app): I minimize a window and send it to the dock but then safari cannot access it.
The spot on the dock looks empty
• Rolling the mouse over the spot shows the name of the window but the window does not respond to clicks
• Under Window on the menu bar I can see the minimized window but cannot bring it back to life
It is especially frustrating when this is a web form because I cannot go back to continue to edit it.
I don't know what triggers this behavior but today it happened to me at least twice.
https://discussions.apple.com/content/attachment/69c296d7-c855-4193-90ac-03b48fe3711a
You got some bigger issue here, or a bug in Big Sur I have seen before. Third party modifications I would assume could cause the issue if no insight.
You can file a bug report here—Apple Feedback http://www.apple.com/feedback
That right side of the Dock is not where things go by default.
Do you have the Safari icon in your Dock where you would expect. amongst the apps..(?) If not fix it there, either drag the icon from the Applications folder or Control click>options>Keep in Dock

Control click the Dock icon you see the minimized.

Full screen mode/Tabs and Mission Control really eliminates any need for minimized
Use Mission Control on your Mac - Apple Support