A number of people who slept in the Iwama dojo, including Saito-sensei, were occasionally awakened at night by the sound of people training. But when they looked around there was nobody there.
Saito-sensei told me about such an occasion where he couldn't get up because he felt that someone was pinning him.
The prevailing explanation is that the sounds are made by obake (ghosts), perhaps including that of O-sensei.
One summer my wife and family were off in Fukushima visiting her relatives. Saito-sensei invited me to live as an uchi-deshi while they were gone, and to sleep in O-sensei's wife's room which is next to the dojo. It was a pretty busy time because I was the only uchi-deshi and had to clean the dojo and shrine and do all the other chores by myself before starting my regular job.
I had heard about the obake and wanted to experience them for myself. I was also interested in paranormal phenomenon and set up a tape recorder with voice activation next to my futon.
In all the time I was there I never heard the obake and the tape recorder never activated. Maybe the obake felt that I was disrespecting them and wouldn't give me the satisfaction of making an appearance?