As Pete pointed out to me, the following is noted in the footnotes to the table on page 20:
The case is still under investigation and nothing we say must prejudice possible legal proceedings. A member or former member of PIRA may have been involved in the killing of Joseph Rafferty in Dublin in April 2005. We have no reason to believe that the murder was carried out on behalf of PIRA. However we believe that members of both Sinn Féin and PIRA were aware in advance of the threat and did not take sufficient action to prevent it.
Similarly Robert McCartney is not counted, since although he was killed by IRA men they don’t believe that the central IRA leadership sanctioned it in advance.