Volumetric-modulated arc therapy (VMAT) with field-extended multi-isocentre irradiation (VMAT-FEMII) is an effective irradiation technique, particularly for large planning target volumes in the craniocaudal direction. A variety of treatment planning techniques have been reported to reduce the dosimetric impact. However, there is no guarantee that unexpected latent systematic errors would not occur. Herein, we report the experience with a rare case that could have led to a serious VMAT-FEMII-related accident. A patient with uterine cervical carcinoma was scheduled for VMAT-FEMII to the whole pelvis and the para-aortic lymph node region. A combination of the two sets of field groups with different isocentres was planned: one to cover the para-aortic lymph nodes and the other to cover the whole pelvis. Measurements based on the pretreatment dose delivery quality assurance (QA) revealed an unexpected overdose of >20% in the field overlap region. This overdose phenomenon is not reflected in the calculated dose distribution in the radiotherapy treatment planning system. Therefore, the plan was altered; a homogeneous dose distribution inside the dose junction was achieved. Several analyses were performed to elucidate the overdosing phenomenon. However, no conclusive answer was found to why non-reflection at the calculated dose distribution was found. The limitations to VMAT-FEMII are primarily related to systematic errors in the positional setup from patient-derived and/or mechanical sources. However, this report highlights a rare case of overdosing caused by inverse optimization and dose calculation. We recommend checking the aperture status of the jaw and multi-leaf collimator at each control point of the treatment plan and using a high-resolution image measurement system on a VMAT-FEMII QA to confirm the dose junction status.