Both circumstantial and DNA evidence relating to some of Kraft's murders have caused many to strongly suspect that not all of the murders attributed to Kraft were committed by one person. The prosecution believed these inconsistencies could only be explained by the presence of an accomplice. It is contended that Kraft would have had difficulty moving around 200-pound (90 kg) corpses. Dumping them from moving vehicles while alone would also be difficult to do unnoticed.

Abrasions and debris found at some of the crime scenes, where bodies had been discarded upon or alongside freeways, indicated that they had been discarded from vehicles traveling at more than 50 miles per hour, and for one individual to perform this act without compromising his driving would be very difficult. Moreover, footprints in the sand close to where the body of John Leras was found at Sunset Beach in 1975 unequivocally indicate two people had carried the youth's body to where it was discarded. In the case of Eric Church, semen samples found on his body were inconsistent with Kraft's blood type, and, while the photographs of the victims found in Kraft's car had to have been processed somewhere, no photo developer ever reported Kraft's morbid images to the police. (Kraft himself had no darkroom expertise or darkroom equipment.)

During Kraft's trial, members of the prosecution admitted privately that they did not charge him with several murders that they were certain he had committed because of facts relating to the cases which indicated more than one perpetrator. Although DNA evidence found upon the body of Church was incompatible with Kraft, investigators had found photographs depicting Church in Kraft's car and his distinctive Norelco electric razor was also found in Kraft's house.