According to the transcripts, the May 29, 1999 comic used to have a header that said:
"We interrupt your regularly scheduled comic to bring you PHANTOM MENACE: SPECIAL REPORT."

The header is present in Megatome 1. So... A conversion error.

Indeed:
http://web.archive.org/web/199911140831 ... 90529.html

According to the transcripts, panel 3 in the September 09, 2001 comic used to have a caption that said:
"Peaceful, despite Dr. Clem's constant attention."

The caption is present in Book 7. So... A conversion error.

According to the transcripts, the March 11, 2002 comic used to have a leading caption that said:
"Hi! I'm Joe Sunday, the guy who helps Pete color Sundays and other various artwork on the site. Pete's turned the reigns of the site over to me for this week and boy-o-boy do I have some fun stuff for you guys!"

This caption is present in Book 8. So... A conversion error.

See also the original: https://web.archive.org/web/20020329131622/http://www.sluggy.com/daily.php?date=020311

In the April 07, 2002 comic,

The 2nd place reader-submitted comic is not properly attributed. And there is a typo in the original, so should it be attributed to L.K. Malnassy or L.K. Malanssy (typo)?

First, the comic is missing its header:
"Sluggy Freelance (Art by L.K. Malnassy)"

Second, the comic is missing its footer:
On the left: "All characters copyright Pete Abrams"
On the right: "Sea of Insanity | http://fractuslux.keenspace.com"

Then, the top of Joe Sunday's dialog is cut off.
The left side dialog is missing: "2nd place belongs to L.K. Malanssy [sic]"
The right side dialog is missing: "And finally our 1st place"

These comics were not included in Book 8, but see https://web.archive.org/web/20020606031958/http://www.sluggy.com/daily.php?date=020407 for the original.

Since the areas cut off contained appropriate attribution, we can assume it is an error and not deliberate --> a conversion error.

The July 1, 2002 comic originally included an extra note below the comic which read:

"These over-explanatory word balloons have been added for the plot-impaired. Because plot-impaired people are everyone's problem."

This footer was included with the comic in Book 8 --> a conversion error.

See also the original: https://web.archive.org/web/20020810154 ... ate=020702
(The mismatch in dates is due to a filler comic that has been rescheduled into one week of filler)

The August 10, 2003 comic originally included an extra note above the comic which read:

"Today's comic is to be sung to the tune of "The Circle of Life" from the movie "The Lion King.""

This header was included with the comic in Book 11 --> a conversion error.

See also the original: https://web.archive.org/web/20051124015 ... ate=030810

The March 2, 2004 comic originally included a title above the comic which read:

""Stick-Additions" Sunday Fix Mamajamma Part 1!"

This title was included with the comic in Book 12 --> a conversion error.

See also the original: https://web.archive.org/web/20050903190 ... ate=040302

The March 3, 2004 comic originally included a title above the comic which read:

""Stick-Additions" Sunday Fix Mamajamma Part 2!"

This title was included with the comic in Book 12 --> a conversion error.

See also the original: https://web.archive.org/web/20061021005 ... ate=040303