When Morty and the park employees make it to the food court of Anatomy Park inside Reuben, Marty complains about a bad smell. However, he's wearing a breathing helmet with external air supply. He shouldn't be able to smell anything outside of that.
The E. coli that attack the train are shaped like bacteriophages, which are viruses. E. coli is a type of bacteria, not a virus.
Jerry's Christmas sweater is miscolored - the red and green zig-zag elements should be reversed to make green Christmas trees. This goof is recognized in the commentary track by Justin Roiland and Dan Harmon.