Pulpectomy is a common treatment for severe carious lesions in primary molars. Care should be taken during pulpectomy of the primary teeth for successive permanent teeth. This case series report aimed to describe the cases of three patients who experienced excessive extrusion of canal filling materials and file separation during primary molar pulpectomy. The presence of separated files or excessive overfilling materials observed around successive permanent tooth germs leads to underdevelopment and may trigger cystic changes owing to abscess formation. The most important aspect is to preserve the unerupted successive developing permanent tooth. Therefore, clinicians should consider the anatomy of the primary molars prior to endodontic treatment, be careful when manipulating instruments during pulpectomy, provide appropriate treatment if iatrogenic incidents occur during endodontic treatment, and perform close follow-up to ensure the successful development and eruption of subsequent permanent teeth.