Plot hole: Near the end when Wadsworth is revealing Whodunnit, he re-enacts the whole evening, when he re-enacts running into the billiard room when Yvette was screaming he says one person was never in the billiard room and that person the person who killed the Cook and when he re-enacted the scene in the kitchen when the Cook was found dead, he says one person wasn't in the kitchen because that person killed Mr. Boddy with the candlestick. But they were only ever in the kitchen and the billiard room once, so that was the only ever time Wadsworth could have realised the murderer wasn't in the kitchen or billiard room. So how come Wadsworth only realised Whodunnit until the end of the film?
Plot hole: When Miss Scarlet and Prof. Plum are at the door, they never ring the bell. But Wadsworth goes to the door to greet them anyway. Wadsworth couldn't know they were outside because at the front of the house is the study on one side and the lounge on the other. There are no windows in the lounge and there is a window in the study but not facing the car park. The lightning and thunder blocked all sound of them parking so Wadsworth couldn't hear that either.
Plot hole: When Mr Boddy suggests the guests all leave the house, he makes a pretty desperate escape attempt, leaving the group stood next to a bag full of weapons (which some of them may have known about) for at least half a minute. Depending on which ending you choose to believe there are a number of reasons why he might want to do this. It certainly made it seem as though he had something to hide or had realised his number was up. Later on in the film Wadsworth reenacts the entire evening and goes into quite meticulous detail about the order the guests arrived, where they sat, who said what etc. He also reveals his knowledge of the passages, implicating himself as a suspect. Yet he never mentions Mr Boddy's escape attempt. It turns out that no murders were comitted in this time. Wadsworth might realise this but the guests wouldn't. Considering he goes off at thousands of irrelevant tangents throughout the reenactment, you'd think something like that needed covering, if only for the benefit of misleading the guests to stop them realising that he (Wadsworth) is actually Mr Boddy. Also, there was plenty of time for Yvette to kill the Cook (even though the weapons hadn't been handed round yet, but that would've come out anyway).
Plot hole: In the end, it was revealed Professor Plum shot Mr. Boddy in the study and the wall (near the fireplace) with the same bullet. Yet when it happened in the study, Professor Plum was sitting on a couch directly in front of Mr. Boddy and wall that got shot was at the other end of the room to Plum's left. The angle for the gun could have not been possible with only one bullet. Bullets are shot directly forward but they can't exactly turn to the left and keep on being fired can they? Even though it was later revealed as someone who took the gun from Plum and the gun went off, he was just lying so nobody else would suspect he was the murderer. Also there are two ways we know only one bullet was fired. One: we can hear only one bullet being fired when the lights were out in the study. And two: there were only six bullets in the gun. One for the singing telegram (6-1=5), one for the chandelier (5-1=4), two for the lounge door (4-2=2), one for Mr. Boddy in the study (2-1=1) and the last bullet was used at the other chandelier at the end of the first ending (1-1=0). So no other bullets could have been fired.