Plot hole: When Renee Russo was reviewing the tape showing the room with the painting to see who stole the painting, and the tape was blank because the heat generated from the suitcase hidden under the bench, why didn't she just back up the tape completely to see who put the suitcase there in the first place? (00:28:30)
Plot hole: When Henry rings Maurice's doorbell to give the bad news about Sarah's fatal illness, Maurice and Sarah are upstairs in the bedroom. Maurice approaches the window and looks down while we see Henry looking up in his direction. That he walks away without trying to make contact makes no sense. (01:13:45)
Plot hole: When the twins go shopping with Brigitte, you will notice that they go to several different stores and bring the clothes they have not bought outside to try on. Don't you think you'd be arrested if you went outside the shop with a garment on that you have not bought?
Plot hole: In the Banker's Office, Bond takes the strap from one of the window blinds to facilitate his escape. Overlooking the large quantity of cable he ties round the belt of the villain and his own belt, there must be an awful lot of strap for one blind to allow him to drop from that high up to the ground (well over 50ft?).
Plot hole: Catherine Zeta Jones says that she needs ten extra seconds after midnight to download the program that collects the billions of dollars from the international bank. In the movie at two different point, she states that after 11:00 PM the device she linked to the clock is gathering an extra 1/10 of a second every minute to allow for ten seconds at midnight. If you take a tenth of a second a minute for 60 minutes, you end up with only 6 seconds. 4 seconds short of the required 10. Some people say she only says "a fraction", but she explains the scenario twice. In one instance, she indeed says a fraction, the other time she definitely says 1/10th of a second, which is wrong.
Plot hole: The timing in the film is way off. Given the hours when JM Inc is open, most of the people there would only get to be Malkovich while he was asleep (yes, films have late-night shootings, but not every night); and Craig and Maxine stay up the whole time, then mess with Malkovich afterwards, then get in for work the following morning without showing any sign of fatigue even though there are less than 2 hours left for sleep.
Plot hole: After the scene of Rachel as a child, there are six days worth of events in what should be five days. Monday Lisa kills herself. Rachel works at photo hut. Tuesday Jesse and Tracy have sex, Walter is hit by car. Wednesday Rachel stands Jesse up because Mark and Eric have come to her house. Thursday Jesse and Rachel's first date - no sex. Thursday again Eric meets with the DA and Jesse and Rachel have sex. Friday is the game and party.
Plot hole: At the end when the gang get home to Andy's room, it's night time and the luggage trolley they drove home in is outside the neighbour's house. The next morning it's still there. But we see an ad with the 'chicken man' looking very sad because he lost Woody and the others. How could he have gone to Tokyo, realised the dolls were missing, then zoomed back to Tri County to do the ad the next day? While saving Woody, the toys explicitly say that Andy is returning home the following morning. They must have made it in one night, or they would have missed Andy's return.
Plot hole: Claude was asked to fill in as a driver for the commodore, however, this is strange considering he obviously doesn't have a driver's license and hasn't driven in over 40 years.