In general terms this refers to a freehold that does not stand on its own patch of land.
If (theoretically) for example you owned a two-storey house, and you sold the freehold to the entire upstairs then this would be a flying freehold. These types of freehold can be very difficult to mortgage as the freehold is worthless if the building below falls into disrepair/structural collapse. Generally leasehold is preferred in this instance.
Historically this might have occurred because the building started out as a low level hovel and has been added to and altered over the years by cobbling new dwellings and rooms for different tenants to and above the original structure.