Hey, thanks for the detailed report and the video.
This is a known issue. Worktree support in Glass (Cursor 3) is still not fully finished. Right now in Glass mode the worktree isn’t created automatically like it was before, and if the agent doesn’t run the internal instruction to create the worktree, it will quietly keep working in the main working directory. I get that this directly conflicts with what the UI shows.
As a workaround for now, in editor mode (not Glass) you can use the /worktree slash command directly in the agent chat. That’s more reliable. More details here: Can't find a way to run an agent on a worktree - #11 by Colin.
Let me know if you have any questions.