Short answer
The risk is significantly higher for the dog that ate the pit. While the flesh is safe in small amounts, the pit contains cyanide precursors and is a serious choking or intestinal blockage hazard. The dogs that only ate flesh are at low risk, but watch for any mild stomach upset. For the dog that swallowed the pit, you need to monitor closely for choking, vomiting, or signs of abdominal pain, and contact your veterinarian immediately for advice.
Nectarine — Food safety facts
Feed with care · Dogs · full breakdown on the linked food page
A piece of flesh is fine. The pit contains cyanide precursors and is a choking hazard.
The full verdict, portion guidance and serving notes are collected on the Nectarine food facts page.