Revealing mistake: When Tomie's head is cut off and her body falls into the wheelchair, look closely - it's clear her body is just a painted mannequin. The skin has a plastic-y sheen to it, and the body itself is entirely too stiff and rigid.
Character mistake: In the beginning scene, the doctor cuts his finger open while performing the operation. However, despite the high risk for infection, especially given the extraordinary circumstances of the procedure, and despite the fact he's a medical professional... he doesn't immediately run to rinse off his wound and change gloves. And you can't argue it's Tomie's supernatural influence, because they haven't even seen her yet.
Continuity mistake: In the first movie, it took quite some time (days if not weeks) for Tomie to regenerate back her full body. In this film, it seems to happen in mere hours after her head is placed into the tank for observation.