In flashbacks to 1935 and 1945, Father McCabe is shown to have known Donald Westphall as a child and to have mentored him as a teenager. However, in Breathless (1984), Dr. Westphall told Dr. Auschlander that he had never met Father McCabe.
In a flashback to 1955, Mark and Ellen Craig are depicted buying their house. However, in The Naked and the Dead (1985), Dr. Craig mentions that they have lived in the house for 27 years, meaning that they would have bought it in 1958.
When two police officers walk into the hospital, returning kidnapped Pete to his father, Dr. Morrison, they don't talk to anyone, and no one, including Dr. Morrison, asks where Pete was found. The cops literally disappear, they are not seen leaving the building.