When 'Ralph' (Sam) clocks in, he uses the bottom time card. When Fred (the dog 'Ralph' is relieving), he clocks out using the top time card. So, when all the clocking is done, 'Ralph's' time card is in the bottom 'In' slot, and Fred's time card is in the upper 'Out' slot. However, when Wolf changes the time on the time clock, there is one card in the lower 'Out' slot and one time card in the upper 'In' slot.
The time clock and cards show up again at the end. When Wolf (dressed as Fred), clocks in, the starting arrangement is not visible. However, when Wolf/Fred finishes clocking in, there are two timecards in the 'In' slots. After 'Ralph' clubs Wolf, the timecards are suddenly reset to have one in the lower 'Out' slot and on in the upper 'In' slot (which is not how they were arranged when 'Ralph' started his shift). Finally, when Fred takes over, 'Ralph' does not clock out.