Rick travels to another dimension to fill Fart's jail cell with water. However, the cell has a massive hole in the side from when Morty crashed into the side of the building.
When Rick and Morty first park in the garage there are three pillows in the backseat. Once the alien appears the pillows are gone and there's misc equipment in its place.
There is no director's commentary for Midnight Run (1988), in our universe/timeline. The copy of the film the Jerrys watch could be from another.