Glad to hear you were successful through a restart to get the computer back to normal.
Sometimes a start up in 'Safe mode' where you could repair disk permissions, then restart
could help an odd issue, where the permissions and privileges may have been mixed up...
If the items in the trash were symbiotic links (such as icons in the Dock) they would have
appeared to be the Macintosh HD, but the Disk Utility could have shown you otherwise.
Such copies or aliases may appear to be disc images that may be ejected. Been awhile
since I had that kind of ghost in the machine; wasn't the real file and wasn't a real copy.
The actual 'Macintosh HD' is a partition on the hard drive, so your copy was likely a link or
an equivalent of an alias pointing to the actual partition. The OS X Recovery's Disk Utility
version probably could have checked+repaired the error; or Safe mode + repair permission.
A curious situation and question; thank you for posting...! 🙂