The diradical state is an important electronic state for understanding molecular functions and should be elucidated for the in silico design of functional molecules and their application to molecular devices. The density functional theory calculation with plane-wave basis and correction of the on-site Coulomb parameter U (DFT+U/plane-wave calculation) is a good candidate of high-throughput calculations of diradical-band interactions. However, it has not been investigated in detail to what extent the DFT+U/plane-wave calculation can be used to calculate organic diradicals with a high degree of accuracy. In the present study, using typical organic diradical molecules (bisphenalenyl molecules) as model systems, the discrepancy in the optimum U values between the two electronic states (open-shell singlet and triplet) that compose the diradical state is detected. The calculated results show that the reason for this U value discrepancy is the difference in electronic delocalisation due to π-conjugation between the open-shell singlet and triplet states, and that the effect of U discrepancy becomes large as diradical character decreases. This indicates that it is necessary to investigate the U value discrepancy with reference to the calculated results by more accurate methods or to experimental values when calculating organic diradicals with low diradical character. For this investigation, the local magnetic moments, unpaired beta electron numbers, and effective magnetic exchange integral values can be used as reference values. For the effective magnetic exchange integral values, the effects of U discrepancy are partially cancelled out. However, because the effects may not be completely offset, care should be taken when using the effective magnetic exchange integral value as a reference. Furthermore, a comparison of DFT+U and hybrid-DFT calculations shows that the DFT+U underestimates the HOMO-LUMO gap of bisphenalenyls, although a qualitative discussion of the gap is possible.