User blog comment:Aithusa07/List of Plotholes from Merlin/@comment-123.2.187.141-20150530162132/@comment-5674726-20150615230426

One note about Morgause: it was never explicitly stated that she had to be smuggled out of Camelot to protect her. She was born before the Great Purge. Uther was led to believe that she died as a baby but that doesn't necessarily mean that he ordered it or wanted it.

Maybe Vivienne, who seems to have had a connection to the Isle of the Blessed, wanted to pledge her first daughter to the service of the Triple Goddess and, as she knew that her husband (who may or may not have been the father) wouldn't go for it, she told him that the baby died.