Nicky and/or Alexander - S5-E11
Other mistake: When Becky first names the twins before leaving the kitchen, Alexander has the peach booties and Nicky has the mint green. When Jesse takes them off and goes to put them back on, he switches these colors, making Alexander mint green and Nicky peach. The next morning, Jesse ends up switching them back to the original, making the baby's identities correct. Later in the episode when he does the foot print and discovers who is who, Alexander is wearing the mint green booties and Nicky was wearing the peach, which was not what the original colors were. So they either still mixed up the babies, or he "changed" the booties other times not shown in the episode.
Chosen answer: The first time was in the first season, episode 19 "The Seven-Month Itch", the second was in the fourth season, episode 1 "Greek Week", the third time was in the fifth season, episode 19 "The Devil Made Me Do It" and finally in the very last episode of the series, "Michelle Rides Again", season 8 episode 23.
jennibee