Intrabony defect around implant and pain?

I have 2 patients that I placed several implants on the mandible and patients continued to experience discomfort for the last 2 weeks and discomfort would not go away. Both patient have been on Amoxicillin 500 every 8 hours and Peridex rinse. The X-rays looked great. I decided to make a flap and see what is going on, after reflecting the flap I noticed intrabony defect around the implants. This happened 3 to 4 days after placement subgingivally. Both implants had final torque of placement around 55-60. Excellent primary stability. I don’t understand why this is happening. Anyone has any information and the reason for this to happen please respond. Thank you and I appreciate any information you can provide.