This behavior is a mix of a known macOS design limitation and an ongoing window restoration bug.
Stage Manager does not save your layout state as a permanent "project workspace". Instead, its groupings are purely recency-based and dynamically derived from active windows. When your Mac boots fresh or wakes from a deep sleep, the underlying macOS WindowServer frequently fails to restore window positions in the correct order. Because the system loads apps one by one upon waking or booting, Stage Manager defaults to its fallback behavior: grouping windows strictly by application and completely wiping out your custom multi-app groups.
The issue becomes even more aggressive if you use an external display, as macOS often temporarily drops the monitor signal during sleep, forcing all windows onto one screen and scrambling your groups when the signal returns.
You can minimize this frustration and build more persistent groupings using the following workarounds.
Settings to Tweak in macOS
Disable App Window Grouping Fallbacks:
Go to System Settings > Desktop & Dock. Scroll down to the Mission Control section and ensure Group windows by application is turned OFF. This prevents macOS from aggressively forcing same-app windows (like your four Finder windows) into a single stack.
More info from Apple: View open windows and spaces in Mission Control on Mac - Apple Support
Prevent Window Closure on Quit:
In the same Desktop & Dock menu, scroll down to the Windows & Apps section and toggle OFF "Close windows when quitting an application". This forces macOS to try harder to remember window states across reboots.
Change Wallpaper Click Behavior:
Under Desktop & Dock, locate Click wallpaper to reveal desktop and set it to Only in Stage Manager or Never. An accidental click on a blank desktop space can mistakenly sweep your custom groups out of view, mimicking a reset
To have Apple consider your feedback, submit it here:
Feedback - macOS - Apple
