The measured D-D neutron rate of NBI heated JET baseline and hybrid H-modes in Deuterium is found to be between approximately 50% and 100% of the neutron rate expected from the TRANSP code, depending on plasma parameters. A number of candidate explanations, such as fuel dilution, errors in beam penetration and effectively available beam power have been excluded. As the neutron rate in JET is dominated by beam-plasma interactions, the 'neutron deficit' may be caused by a yet unidentified form of fast particle redistribution. Modelling, which assumes fast particle transport to be responsible for the deficit, indicates that such redistribution would have to happen at time scales faster than the slowing down time and the energy confinement time. Sawteeth and ELMs are found to make no significant contribution to the deficit. There is also no obvious correlation with MHD activity measured using magnetic probes at the tokamak vessel walls. Modelling of fast particle orbits in the 3D fields of NTM's shows that realistically sized islands can contribute only a few % to the deficit.