Holmes refers to the rock containing the fossil as an archaeological item, but archaeology revolves around the study of human past and development rather than dinosaurs. Hence, the rock containing the fossil would instead be considered paleontological.
The extinction event that killed off the dinosaurs, known as the Cretaceous-Paleogene extinction event, was not the largest extinction level event in history. It saw about 17% of all families, 50% of all genera and 75% of all species wiped out. The largest extinction level event was the Permian-Triassic extinction event. It saw the end of 57% of all families, 83% of all genera and 90-96% of all species on Earth at the time.
When the rock containing the fossil is found smashed at a crime scene, there are pieces of white bone interspersed among the black rock fragments. This is impossible as fossil bones are essentially part of the rock they are contained in and must be extracted by carefully carving the rock away from the fossil. If the rock had been smashed, the fossil would have fractured along with the rock, not been broken out of the rock. The fossil would also not be white as it is also technically rock due to the process of fossilization converting the bone to minerals, and so the fossil would be a dark stone color.
Gay states the rock dates to 65 million years ago, in the Cretaceous Era. The Cretaceous lasted from 145 to 66 million years ago. The Paleocene lasted from 66 to 56 million years ago, so 65 million years ago falls into the Paleocene. One assumes the writers used Cretaceous because the name is more recognizable to the general public than Paleocene.
It makes no sense for Watson and Homes to use a mixture of nail polish remover and black coffee just to remove marker ink. The nail polish remover is so aggressive it could damage many surfaces, especially (like here) a photo. Coffee adds little to no cleansing effect, and if you need some acidity, you would of course just use an acid, lots of which are clear liquids. The first thing you try is alcohol, a very mild solvent that will do the job just fine in the vast majority of cases.
Whether in Latin or in English, Holmes' forged pages of Luther's writings would be recognized as fake at a glance. Handwriting from 500 years ago looks very different from today's handwriting, so much so that special training is needed to decipher it and even more training to write in it. Holmes should have been aware of this, but does not mention it, and the pages that are shown on screen use a modern handwriting style.