I have a Late 2020 Mac mini running whatever the latest 11.x.x is. It's hooked via HDMI directly into a 32" Asus monitor. Whenever I restart - which isn't common - or wake the computer from the display being off (not the computer asleep because I have weather software connected to a weather sensor that uploads to Wunderground), windows move and resize, typically moving to the bottom-left ≈1/4 of the display, as though the OS doesn't detect the monitor right away and tries to move things around to compensate.
This phenomenon is hit-or-miss depending on the application and depending on whether it is hidden or not. So, I just tested it again, and Safari, Finder, Keynote, and Excel all stayed put (not hidden). But, VLC moved. Then, if I do something like hide Safari and put the display to sleep, then wake it up, all my Safari windows are on top of each other in that bottom-left ~quarter of the display.
I'm a bit OCD with where I place windows and how I have them sized, so it's a fairly continuous frustration not being able to hide things when working on certain tasks or needing to move stuff back after coming back to the computer, and then if I do forget and hide something needing to re-move and resize them all when I come back.
I thought this might be an issue with the M1 chip, or the macOS 11, but we're now over half a year in and this is still a major issue for me, so maybe someone can help? (I've not owned a Mac mini before, but I've had several headless Mac desktops and this was never an issue)