Killing a shared buffer in two workspaces results in a buffer leak

### I confirm that...

- [x] I have searched the [issue tracker](https://github.com/doomemacs/doomemacs/issues), [documentation](https://docs.doomemacs.org), [FAQ](https://docs.doomemacs.org/-/faq), [Discourse](https://discourse.doomemacs.org), and [Google](https://google.com), in case this issue has already been reported/resolved.

- [x] I have read "[How to Debug Issues](https://doomemacs.org/d/how2debug)", and will use it to provide as much information about this issue as possible.

- [x] The issue can be reproduced on the **latest** available commit of Doom.

- [x] The issue can be reproduced on a stable release of Emacs, such as 27, 28, 29, or 30. *(Unstable versions end in .50, .60, or .9x)*

### Expected behavior

I have two workspaces and a shared buffer, e.g., test1.org, and in workspace 2 I have another buffer test2.org. When I close test1.org in workspace 2, test2.org should not appear in workspace 1.

### Current behavior

When I close the buffer test1.org in workspace 2, test2.org appears in workspace 1.

https://github.com/user-attachments/assets/1ea11dca-6be4-436b-948c-a2677b7515c4

### Steps to reproduce

1. Open emacs, find a file called test1.org.
2. Create a new workspace.
3. Find file test1.org and test2.org.
4. Delete test1.org buffer.
5. Switch back to previous workspace, and the test2.org buffer is there.

### System Information

https://pastebin.com/EKUzcX2i