Revealing mistake: After the old lady steals the meteor rock from Luigi, the big lady in red picks her up and throws her off down below into a moving car. She gets up and shocks the driver, causing the car to rear end the vehicle in front of it. If you watch closely, you see the engine top shift forward and the back of it lifts up. This reveals it is just a fake prop attached to the vehicle and not a real engine.
Revealing mistake: In the prison escape scene, Mario and Luigi get on a zip line like pulley track and swing though the prison. Goombas are shooting fire balls at them. The first fire ball slowly goes and hits a wall. Watching closely, you can see the line of fire travel down the wall, showing where the special effects crew had pre-coated the wall with a flammable fluid.
Revealing mistake: During the car chase, when Mario and Luigi have the cops on either side shooting the guns, Mario screams "Brace yourself, now!" When he says this, you can quickly see Mario and Luigi have been replaced by stunt drivers. Also, Mario's mouth isn't moving. It happens quickly, so slow motion helps, but isn't required.
Revealing mistake: When Mario and Luigi's police car drives off the civilian's car they're stuck to the top, you can blatantly see a metal special effects line that's pulling their car down.
Revealing mistake: When the old lady falls into the car, she blatantly turns into a dummy for a few shots. (She literally doesn't move at all and is unnaturally stiff.)
Revealing mistake: When Mario and Luigi first arrive in "Dinohattan" and fall through the railing, you briefly get a clear look at Luigi's stunt-double, who appears to be a bulkier man who looks nothing like John Leguizamo. It goes by quick, so it can be hard to see, but once you notice, it's obvious.
Revealing mistake: When Daisy takes Luigi to the dig site, there's a long wide shot as they talk and start to head down. As the camera zooms in, you can see the composited background (the bridge, city, etc.) "jiggle" slightly towards the end of the shot where the composite effect didn't quite align up.
Revealing mistake: In the opening, when Daisy's mother pushes the beam and causes the cave-in in the mine, for a split second, you get a pretty clear shot of Koopa's stunt double, who is taller than and looks nothing like Dennis Hopper. He's only on-screen for about a half-second, but it's very easy to notice it.
Revealing mistake: When the meteorite strikes the Earth at the beginning of the film, there's an odd slip-up in the effect. About a half-second before it hits, you can sort of see it awkwardly shift slightly to the right for a split second. It's hard to catch, but once you see it, it's fairly noticeable.
