When Howie listens to Willow singing while nude, he grabs a picture on the wall and leaves it hanging crooked. As he steps away, it is straight again. When Willow comes into his room the next morning, the picture is crooked again and she straightens it.
There is a cut when Rowan Morrison's coffin is exhumed, during which Sgt. Howie moves visibly closer to the gravedigger and the ropes around the coffin disappear.
As Sergeant Howie is crossing the causeway to the sweet shop, you see a person on bike cycling towards him, but a few seconds later, the bike has vanished without enough time for the cyclist to get out of the way.
While Sgt Howie is at the chemist shop he shows Lennox (who is mixing something with a mortar and pestle) a photo of the missing girl. Notice how in between shots the photo goes from Howie's hand into Lennox's hand, without having been handed over.
When Sgt Howie inspects the school register he stops on "Belthane Term", where Rowan Morrison's address is given as "The Tuck Shop." The shot changes to a close-up, and his finger runs along the same page to now find she was resident at "The Post Office." His hand is also clearly in the wrong position on the following change.
The calendar in the Photographer's shows May Day to be a Tuesday, therefore Sergeant Howie flew out on Sunday. Not only is this notably unlikely for a routine police investigation in the generally religious Scottish Highlands, The Director's Cut shows Howie receiving the letter on the same day. There were no Sunday postal deliveries at the time.
Most of the "naked" girls dancing in the stone circle and jumping over the fire are wearing flesh-colored body stockings (the film was shot in autumn and not in spring as it was set, and thus was very cold).
At one point during Willow's nude dance, she rears her head back and her face is slightly visible, just enough to see that it's obviously a double.
While Sgt Howie (dressed as Punch) is being chased by the women, you can see autumn leaves on the grass, though the story is set on the first of May.
In the scene where Sgt Howie hits McGregor (who is dressed as Punch) with a candlestick, watch closely and you can see that the blow from Howie is aimed into the padded section on the back of the punch costume, rather than at the back of McGregor's head.
One of the chemicals in the chemist's shop was dimethylglyoxime. While that is a genuine chemical, its uses are highly specialized (analyzing nickel and palladium compounds, and in the production of some chemical weapons), and it would be unlikely to be found in an isolated chemist's shop.
When Sergeant Howie is in the pub for the first time, there is a close-up of the cash register, showing 3d in the window. The movie takes place in 1973, and decimal currency was completed two years earlier in 1971. (It's possible a remote island and its equipment might be slightly out of step with mainland Britain.)
During the scene in which the boys are dancing and singing round the Maypole, none of the children's lips are moving although we hear singing on the soundtrack.
When Sgt. Neil Howie is captured, the quote: "There will be no traces. Bring him up, Oak," that has begun spoken by Lord Summerisle where he is nearly hidden on the left along with the rest of the cult villagers surrounding Howie, his lips do not move. The next cut image, however, sees him speak the rest of the line.
Despite being set in the Scottish Highlands, and the Hebrides, many of the traditions alluded to are English, rather than Scottish.