We investigate energy leakage induced by incomplete measurements of the scattering matrices of complex media. Owing to the limited numerical apertures of an optical system, it is experimentally challenging to access theoretically predicted perfect transmission channels in the diffusive regime. By conducting numerical simulations on scattering matrices, we demonstrate that energy leakage contributed from uncollected transmission in the transmission matrices provides an energy transmission that is more enhanced than that predicted by measurement. On the other hand, energy leakage originating from the uncollected reflection in the partial measurement of a reflection matrix strongly suppresses the energy transmission through a zero-reflection channel, restricting the transmission enhancement to no more than a fivefold enhancement in limited optical systems. Our study provides useful insights into the effective control of energy delivery through scattering media and its ultimate limitation in practical schemes.