Messup one is the alternating "butterfly" design on the ballot as shown in the image. It was deemed too confusing because the candidates aren't listed in a single order.

Messup two is a hole punch was used to punch holes in the central area on the ballot, but it wasn't very good at its job. The hole punch system left a bunch of ballots with only partially punched holes, and "hanging chads" where the punched out piece of paper is still attached and dangling. During the recounts the election board had to make a bunch of individual decisions on how to interpret these ballots.