I'm on 12.7.6, perhaps this is associated with behavioral changes in later macOS releases.  Do you have an example of another application you switch to when you see this behavior?  I switch to Chrome or another Emacs session or Terminal.app and back and I don't see the issue.  The window I last selected remains selected and if I click in any other window, that one is correctly selected.  I tried again both with my configuration and on master with -Q and it seems fine.

On Sun, Mar 2, 2025 at 5:06 PM Daniel Colascione <dancol@dancol.org> wrote:

On March 2, 2025 4:41:59 PM EST, Ship Mints <shipmints@gmail.com> wrote:
>I use the NS builds, both as my production (now 30.1) and from master, and
>I do not see this behavior. Do you have implied window selection features
>enabled like focus-follows-mouse or mouse-autoselect-window? Do you use
>any mac applications or helpers that might be interfering?
>

Don't know why you're not seeing it. Apparently macOS is supposed to behave this way unless you override <https://developer.apple.com/documentation/appkit/nsview/acceptsfirstmouse(for:)>, which I have made Emacs do