First, Sophie's "death" - to pull it off would have required the cooperation of at least her family (not likely), as her death would have required a funeral and burial.
Second, the evidence Uhl found in the stable. Enough time passed between the murder and the search that the stable would have been cleaned out - especially in a "royal" stable, and especially the straw.
I loved this movie but the plot holes are just hard to ignore. In real life, there would have been far too many people involved in the autopsy and investigation of a murder of a Duchess no less.
Being in cahoots with a single coroner would not nearly have been enough to fake the death of a woman of that stature. First of all they would have taken her to a morgue. Autopsies are not conducted on the crime scene by one person and the body then shipped away after 5 minutes. The chief inspector barely glanced at the body which is of course ridiculous.
The team of investigators and doctors would have to be total buffoons to be tricked that someone is dead. The lacerations on her neck would have to be prosthetics otherwise the Duchess would REALLY be dead with that kind of injury. And then that miracle drug that takes away all signs of life doesn't exist even in today's world. Doctors can put you in a coma but of course you will still have a heartbeat and a pulse. And even if this was plausible, how long could she survive like that before being woken up again?
This movie is set sometime in the 19th century, long before cars, dna-testing or even fingerprints. What kind of scientific methods do you think they had? That was the era of the prim and proper and it certainly wasn't proper to cut up a duchess like a fish, even in a murder investigation.
You're obviously mistaking the 19th century for the Stone Age. Maybe you should read up first on the history of medicine, anatomy, and autopsy before you make a condescending reply. Autopsies have been done for more than a thousand years. One famous example is a certain Julius Caesar Emperor of Rome, who was autopsied after his assassination in 44 BC, leading to the conclusion that the second stab wound was the cause of death.
In fact the methodology hasn't changed much since the 19th century. The point still stands, a 19th century doctor would have to be a complete buffoon to mistake someone for dead.
The doctor was no buffoon, he was in on the whole thing! He knew the duchess was still alive (though drugged), that's why he interfered when the inspector touched and looked at her fingers, accusing him of treating her 'corpse' like a sideshow freak. Most likely he feared the inspector would feel her pulse or any other life sign. As for an autopsy, it would be easy to switch Sophie with another corpse, someone with similar features and wounds.