The check against the atlas at home was just that - a check to get the best idea of where he was going. The issue is that those co-ordinates were changed the night before they left, so all of Collins' crew thought they were on the McMurdo Sound track that had been discussed at the briefing with Captain Simpson (of the previous flight) and his crew.
The data sent to McMurdo by ANZ that morning was also incorrect - the co-ordinates for the waypoint simply substituted with the term "MCMURDO", so a second chance to catch the error was missed.