After everyone goes to bed, Poelzig enters Werdegast's room to "settle" things. But Alison and Werdegast have switched rooms. Werdegast enters the room to reveal this fact and is wearing only pajamas. Werdegast and Poelzig then exit the room. When the scene cuts to Werdegast's room, he is now wearing a robe.
When Werdegast and Poelzig are fighting near the end of the film, Poelzig is on top of Werdegast, choking him. Werdegast then turns the tables and ends up on top of Poelzig. After Thamal (Werdegast's servant) enters the room, Poelzig is suddenly on top of Werdegast, and is choking him again.
Vitus identifies Kurgaal as being "near Omsk, by Lake Baikal." In reality Omsk and Lake Baikal are approximately 1000 miles apart and are nowhere near each other.
One of the women in Poelzig's glass coffins visibly moves while he is admiring her.
None of the organ music matches the notes the characters are playing. This is most visible when Karloff is playing Toccata and Fugue in D minor late in the film.
The sounds of the explosions do not match the visuals in the long shots of Poelzig's house as the undermined dynamite explodes.
"And this is the old chart room for the long-range guns. The guns are gone but the charts are still here." As Poelzig speaks these words, his mouth is not moving.
Vitus was a prisoner of war for 18 years and he says he just got out of jail that day, and traveled a long way to get to Hjalmar's house; so, even if on the way, he's grabbed a calendar to figure out which phase of the moon it is and he has inquired in town where Poelzig lives, there is no way for him to know that, in 18 years, his former friend has become a satanic priest and that the very night he is holding a sacrifice ceremony for the Dark of the Moon ritual.