As I understand your post, you did an Edit/Cut on a selected clip in the timeline, and it did disappear from the timeline, but on playback it still appeared in the preview screen. So, in other words, it remained as a ghost clip. Is that correct?
You might try deleting/resetting preferences and see if that cures it. To delete/reset preferences open iMovie while holding down the Option and Command keys and select to delete preferences in the box that appears. iMovie will open in a new empty library. Reopen your old library to get back to your
projects. Possibly you may need to reboot to set the changes. Deleting preferences is a safe procedure that
will not cause data loss or disruption to your project.
You might also try doing an Edit/Select All, Edit Paste of the project media into the timeline of a newly created project to see if you can get rid of the ghost clip. Your edits will carry over.
Finally, sometimes a simple reboot the computer will cure some odd issues.
-- Rich