When Kooky's time machine is working, it's on the floor right by Kooky. Then when Koopa is running to the steering wheel of the doom ship and calls Kooky a "slow poke," the time machine is gone. Then when the crate with Mario, Luigi, and Toad slides down the cock pit when the ship tilts, the crate slides and as it hits the time machine, the machine is in the middle of the cock pit.
As the doom ship is taking off in Brooklyn, Toad (still as a baby) jumps onto the ship. In the next shot when he's climbing in, he's back to his regular adult self. When he retrieves the time machine to transform Mario and Luigi back to their adult selves, Toad is also back to his adult self. He wasn't shown being transformed back to his regular adult self.
As Kooky carries the customer lady's furniture to the restroom door, the furniture clips through the door, disappearing, instead of passing behind the opening.
The crate which Mario, Luigi, and Toad are hiding in gets placed on the floor in the cock pit of the doom ship. When Koopa goes to the crate to investigate the squeaky sound Toad makes, the crate is show to be placed on the lower part of the wall and not touching the floor.
(at about 8 mins) As Luigi and Toad were seen loosening the valves to the water supply, the 3rd valve, to the right, had nobody open it, and yet it pumped its water as soon as Toad's and Luigi's did.