Punctuated equilibrium does not contradict Darwin’s initial theory.
"The geological record is extremely imperfect and this fact will to a large extent explain why we do not find intermediate varieties, connecting together all the extinct and existing forms of life by the finest graduated steps. He who rejects these views on the nature of the geological record, will rightly reject my whole theory."
--Charles Darwin, The Origin of Species by Means of Natural Selection or the Preservation of Favoured Races in the Struggle for Life, reprint of 6th edition (London: John Murray, 1902), p. 341-342.