If the car is running, driving, shifting fine, the swap itself is done well, then it's just a major oddity. Even if it came with a 6 speed, and it somehow failed, to swap in a 5 speed...the mind boggles
If it was an automatic, and the owner wanted a manual, it's still odd unless they had a 5 speed already, and the skills to swap...
I just don't know. Have you eyeballed the transmission, driveshaft, rear end? Not sure if anyone could identify by the pan bolt pattern, etc.