
Continuity mistake: Right before Ben jumps off the cliff, he drinks a small cup of coffee and places it back on a saucer that Jonathan is holding. When the shot cuts, the saucer is still visible in Jonathan's hand, but the cup cannot be seen on it. The cup then reappears in the next shot.
Chosen answer: During the several years it took to construct the ship probably, or in any of the supplies/food brought on board, or in the furniture brought on board. A single pregnant female rat can be responsible for thousands of rats in a very short space of time (the offspring are not too choosy about who they breed with).
Soylent Purple
A pregnant female rat could have made a home in a underneath a third class couch and had the other rats then all the females would have baby rats quickly.