That's one of many fundamental problems that have emerged. The theory was a lot easier to fit into limited scientific knowledge 150 years ago. The central prediction was that all species slowly, gradually, smoothly morphed from the simplest form, into life as we know it today. The vast gaps in the fossil record could be assumed to be mere artifacts of an incomplete record, to be filled in later as we go..
150 years later and this central prediction could hardly have failed more conclusively, by Darwin's own standards. we have even less transitional examples than we did then, the gaps were not filled but in constrast have been ever more clearly defined.
Instead of Darwin's predictions, we see highly evolved species appearing overnight, all over the planet, remaining unchanged for periods of sometimes hundreds of millions of years, and suddenly disappearing, to be suddenly replaced with a set of new highly evolved species.