At about 7:30, when a hole is blasted in the ship, Holo-Lincoln is seen floating outside along with the other holo characters, yet minutes later (at around 50 mins) he is seen hanging out with the gang.
As Kif gasps in surprise at learning he is pregnant, he is wearing both gloves. Yet, immediately before and after, Kif is missing his right glove, which was sucked off the ship.
The hole that gets plugged by the moon disappears in later exterior shots of the Nimbus.
It would have been impossible for Amy to have hidden herself in the pain pill capsule and then putting all the little medicine balls back inside of it.
During the long delivery trip, Leela says the crew have to go into "hybernative naptosis" to save oxygen. However, they are then shown simply sleeping in their quarters which means they would still be consuming oxygen.