When Emmanuel comes in out of the heavy rainstorm, his hair is dry and his cloak shows only a few wet spots.
When Dr. Hildern draws a blood sample from the severed finger, he only pulls what amounts to a few drops into the syringe. Minutes later, when he combines his own blood with that from the sample, the syringe is now about 1/4 full.
When Emmanuel visits Dr. Hildern after the death of his wife, a book stand appears out of nowhere between cuts, to the right of Hildern at his desk.
When professor Hildern (Peter Cushing) reads the letter from the asylum about his wife's death the letter is ask white. Later when Penelope (Lorna Heilbron) reads it in her mother's room the letter now has a black border around the edge.
Towards the end of the film, when the creature is approaching Emmanuel Hildern's house, the creature's shadow is cast on the front of the house, meaning the creature is between the house and a source of light. However, its shadow grows larger as the creature moves, which suggests that the creature is actually walking towards the source of light and away from the house, rather than the other way round.
Marguerite's bedroom has been locked for the last 15 years or so. Her shoes & hatboxes are in disarray as if they were knocked over when she was forcibly taken to the asylum long ago. But there is no dust on anything, not even her feather boa or powder puff.
When Professor Hildern describes where he found the skeleton, he points to a map of "Australian New Guinea". The movie takes place in 1893, but Australian New Guinea did not exist until 1914. The region was known as British New Guinea from 1888 until 1902.
When the creature appears alive, there is no explanation for where its clothing came from.