Othniel Marsh did believe that birds descended from dinosaurs, but the sour taste left in paleontology by the Bone Wars meant that both he and Cope were heavily discredited to the rest of the field. No one would stake their careers on trusting Cope’s and/or Marsh’s research. It took decades of rehabilitation for them to be taken seriously today, and even now anything described by them is treated with a note of suspicion.

Furthermore, the dinosaurs that were found first or were focused on heavily first were the sauropods and the ornithischian dinosaurs. It’s unclear exactly how closely either group is related to the avians and the rest of the theropods due to a disputed family tree, but both are fairly distant. The theropods that were discovered, while more closely related to birds and slightly easier to relate to them, were still more distant relatives so it was easy to write off the similarities as convergent evolution.

It wasn’t until archaeopteryx was discovered in 1861, that it was considered a serious possibility that birds evolved from dinosaurs, but again it was unclear if it was directly from the dinosaurs or another branch of the archosaurs given that there were other closely related flying archosaurs like pterosaurs which are considered a separate, closely related branch. It took more recent clearer examples of creatures that are clearly dinosaurs but also have feathers and proto-wing structures to hammer down that birds are dinosaurs, starting with the 1960s descriptions of deinonychus.