In summation, the Zodiac Killer wrote the original draught message of 408 alphabetical letters (including Z} in a continuous 17 by 24 grid formation, knowing that he had to begin to encrypt the Chronicle portion starting with the alphabetical letter "E", ending "TH" from the Examiner portion, in order to form the word "THE". Unfortunately, he didn't encrypt the next line of ELONEORSTRAYPEOPL contained in his draught message, he mistakenly missed this line and encrypted EIHAVEKILLEDWILLB, which also began with an "E". Hence, he failed to encrypt one line of the Chronicle plaintext message, leaving him with an unwanted line at the bottom of the cipher. This is the possible filler line, created for apparent symmetry. Whether the Zodiac Killer crafted another message in the bottom line (in response to his mistake) is unknown to this day.
The Missing Line in the 408 Cipher covers this story in more detail, but I wanted to create a full image of the cipher for reference.
As always, thanks to Dave Oranchak for originally suggesting the concept of a missing line.