When Alistair Ravenscroft is talking with the dying Margaret at the bottom of the cliff, the light from the lighthouse crosses them at irregular intervals. In reality, the rotating beam from a lighthouse would cross any given point at regular intervals.
They don't explain how the crazy twin sister got pregnant and with who. Also, they don't explain how the crazy twin sister's daughter came to be at the house when the crazy twin sister's brother-in-law told the help lady that he was going to kill the crazy twin.
When the police drain the bathtub where the doctor is, you can see the actor involuntarily wiggle his mouth to keep the cloth inside it.