He was involved in litigation in 1889 with his old assistant Charles A. Borst, and the "Great Star-Catalog Case" "Peters v. Borst" went before the Supreme Court of New York. The judge sided with Peters, but many astronomers and newspapers sided with Borst. Peters died not long after the trial end. After his death, the judgement was ultimately reversed on appeal and a new trial was ordered, but it never took place.