There is no contradiction at all. Most of the Annullments are of Protestants.
It is generally accepted that there are about 6 million Catholic marriages (sacramental and non-sacramental) involving Catholics which have been sundered by divorce in the courts over the past 35 years (for some persepctive, 20 million marriages have been contracted in the Church the period 1943 to 2002). It is also generally accepted that only 10% of these have ever availed themselves of a Church annullment. Yet, in the past 35 years, there have been around 2 million annullments granted by the Catholic Church in the US.
600,000 << 2,000,000
It implies that around 2/3 of all annullments granted since 1968 have been to non-Catholics, which is independently confirmed by the testimony of people involved in the tribunals.
Additionally, about 1/4+ of the annullments granted are documentary annullments. These are simply given out when a Catholic comes along and can show invalidity from things like marriage by a justice of the peace, in a Protestant Church without dispensation, to an inelligible person, etc. These cases are simply indisputable as being invalid canonically.
Put 2 and 2 together, and you will realize relatively few of the non-documentary annullments are granted to dissolve putitative Catholic marriages, such as those of the Kennedy's.