Similar thing happened to me many years ago.
Newly valid civil tower controller. Having left the RAF and experienced run and breaks from fast jets every day at work.
Had a call from a spitfire requesting run and break which I approved. Incorrectly, I assumed that would be at regular circuit height as per ex RAF days. Nowhere, anywhere, in any document does it say 'run and break' means a clearance to use the runway. Just my opinion perhaps, but ''line up, take-off, back track, land, touch and go or low approach and go around' means the aircraft can use the runway. Not 'run and break approved'!!
Therefore lined a 757 up in anticipation of the spitfire breaking in the overhead at 1000ft and clearing the climb out fairly promptly. Imagine my surprise when said spitfire then drops to maybe 100ft and passes down the right hand side of the 757.
Inexperienced at the time I summed it up as my lack of knowledge. Years later now and having a bit more gumption, I certainly would have enquired as to exactly what the spitfire pilot's understanding of the term 'run and break' meant. Clearly considerably different from what most of us controllers seem to think.