Yes, both editors keep their own in-memory copy of open files and their own idea of what the agent "last saw". If agent A writes a file while editor B has an unsaved or stale buffer, B can save its old version on top. Autosave makes it worse.
If you want two agents at once, give each its own folder:
git worktree add ../myapp-ui ui-workOpen Windsurf on myapp, Cursor on myapp-ui, merge the branches when done. Or simpler: one agent at a time, other editor closed.