The hole wasn't dangerous to the crew on re-entry because the section of the capsule it appeared on was jettisoned before re-entry into Earth’s atmosphere.
Prokopyev said in a news conference that the hole was made from inside the dock, and "it's up to the investigative organs to judge when that hole was made."
Russian space agency Roscosmos chief Dmitry Rogozin said in September the hole could have been drilled when the capsule was manufactured or in orbit. He stopped short of blaming crew members, but the statement has caused tension between Roscosmos and NASA.
Rogozin has since said the media twisted his words.
When asked if the hole could have been drilled by an astronaut, Prokopyev replied, “You shouldn’t think so badly of our crew.”