Complications that occur after maxillary sinus floor augmentation (MSA) can be divided into early and late complications. Early complication is a side effect that occurs during the MSA procedure or during the initial healing period. Usually, late complication refers to a side effect that occurs after 3 weeks of MSA. However, in the longer term, there are cases that occur during the follow-up period after the prosthesis is delivered, and most of them present with peri-implantitis. In the present two cases, sinus graft complications occurred 1–2 years after prosthesis delivery but were independent of peri-implantitis and had atypical features showing asymptomatic results. Although the route of the infection source is unclear, the lesions were presumed to be caused by slow and delayed inflammation of oral bacteria infiltrating the bone graft area of the maxillary sinus. Within the limitations of present case reports, bone defects were successfully managed with a guided bone regeneration (GBR) procedure that included thorough defect degranulation, surface decontamination of exposed implant, and regrafting. Periodic monitoring of radiographic images is required for the detection of unusual sinus graft complications in sinus-augmented sites.