"Why then is not every geological formation and every stratum full of such intermediate links? Geology assuredly does not reveal any such finely-graduated organic chain; and this, perhaps, is the most obvious and serious objection which can be urged against the theory. The explanation lies, as I believe, in the extreme imperfection of the geological record. In the first place, it should always be borne in mind what sort of intermediate forms must, on the theory, have formerly existed."No problem, as long as you assume that they must have existed. Skeptics of the theory would call this "speculation."-Charles "Chuck" Darwin
The Origin of Species (1859)
Your 288: I think Darwin thoroughly refuted himself a century and a half ago when he said that the theory of evolution would be disproved if the fossil record did not, in the century to come, show itself to be replete with transitional forms.
Darwin:
The explanation lies, as I believe, in the extreme imperfection of the geological record. In the first place, it should always be borne in mind what sort of intermediate forms must, on the theory, have formerly existed...What would be the problem with admitting that Darwin didn't say what you reported he said instead of all this dancing around? He said something quite the opposite of what you reported in 288. He had already figured out that the fossil record did not, would not, and should not contain every transitional that ever lived, despite the necessity that such things must have once existed. His chapter on the imperfections of the geological record is explicit from the beginning to the end about what he does and does not predict.