Incidence and clinical results of intraoperative flap and interface-related complications were investigated after Femtosecond-LASIK surgery, where flap creation was performed with VisuMax ® femtosecond laser. A retrospective 10-year cohort study was conducted including all eyes treated for all refractive errors by Femtosecond-LASIK technique. All the flaps were made by the same refractive surgeon with the VisuMax ® (Carl Zeiss Meditec) femtosecond laser. We report the intraoperative flap and interface-related complications in these eyes, also describing their management. The study included 4,032 eyes. Flap and interface-related complications were: opaque bubble layer (OBL) 21.18%, suction loss 1.29%, difficult docking 0.69%, difficult dissection of the flap 0.59%, bleeding from limbal blood vessels 0.35%, de-epithelialization of the flap 0.12%, and interface debris 0.025%. These situations were appropriately addressed, with favorable outcomes. Flap creation is an important step in LASIK surgery. The predictability and safety have improved since the flap incision is assisted by a femtosecond laser, but complications of the flap and interface can still occur during the flap creation. Refractive surgeons should be aware and properly manage any unusual situation.