When Orion is open on macOS, Stage Manager appears to get bugged in such a way that it behaves as if the window is over top of the Stages.
With Safari and Firefox open:
With Safari and Orion open:
This behaviour is more or less what Stage Manager does if an app window is maximized or is over top of the Stages but as you can see, the app window is not.
I will add that it behaves this way even if Orion is 'closed' and there is no active window (Command + W) but not fully quit (Command + Q). Stage Manager only behaves normally when Orion is fully quit.
This is somewhat recent but I couldn't tell you exactly which version this appeared.
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0.99.127.3
Sonoma (14)