Two biggest issues so far:

Mobile support is garbage. Navigating the archive books pretty-but-so-impractical 3d thing is impossible, and the chapter headers get cut off on portrait when you do finally get in.

Also with comics coming ad-hoc, I really want email alerts or notifications or SOMETHING so I know when to come back now.

Overall I just gripe about the dated style, I was hoping for something cleaner and HTML5 with solid navigation functionality, like html5up. But that's the dev in me maybe. Having to scroll down the huge 20+ banner every time now just grates on me.

The site needed a facelift, I just hope it's not another 20 before it gets it again to get closer to something workable.

Chapter 49, some inconsistency in a set of filler strips.

This first one looks correct:

http://archives.sluggy.com/book.php?cha ... 2006-05-26

This second one hasn't been embiggened:

http://archives.sluggy.com/book.php?cha ... 2006-05-28

This third one looks like it's been enlarged too much and now no longer contains the text explanation of its context/purpose above and below the panel:

http://archives.sluggy.com/book.php?cha ... 2006-05-29

Chapter 50, this set of strips isn't embiggened properly:

http://archives.sluggy.com/book.php?cha ... 2006-11-09
http://archives.sluggy.com/book.php?cha ... 2006-11-13
http://archives.sluggy.com/book.php?cha ... 2006-11-14
http://archives.sluggy.com/book.php?cha ... 2006-11-15
http://archives.sluggy.com/book.php?cha ... 2006-11-16

Also, this one has a little bit of the next strip at the bottom:

http://archives.sluggy.com/book.php?cha ... 2006-09-26

Chapter 52, these strips have some of their previous strips at the top:

http://archives.sluggy.com/book.php?cha ... 2007-06-11
http://archives.sluggy.com/book.php?cha ... 2007-06-13

Chapter 57, Yarncraft

This strip has some of the next strip at the bottom:

http://archives.sluggy.com/book.php?cha ... 2008-07-29

This strip isn't embiggened:

http://archives.sluggy.com/book.php?cha ... 2008-08-12

This one has a bit of the previous strip on top:

http://archives.sluggy.com/book.php?cha ... 2008-08-13

Some weirdness involving these two strips:

http://archives.sluggy.com/book.php?cha ... 2008-08-14
http://archives.sluggy.com/book.php?cha ... 2008-08-17

The second one looks to be the right size, but the top and bottom of the strip are cut off. The former one look to be not the right size, at least in comparison.

This strip is completely incorrect:

http://archives.sluggy.com/book.php?cha ... 2008-08-28

It should be the Yarncraft Jewel Box thing but is instead a badly cropped reprint of the Winter box (http://archives.sluggy.com/book.php?cha ... 2008-08-23).

Likewise, this strip:

http://archives.sluggy.com/book.php?cha ... 2008-08-30

Should be the Winter box printable but is instead a repeat of the normal box printable (http://archives.sluggy.com/book.php?cha ... 2008-08-26).

This strip:

http://archives.sluggy.com/book.php?cha ... 2008-08-31

Should be the Kids box printable but is instead a repeat of the normal box printable (http://archives.sluggy.com/book.php?cha ... 2008-08-26).

Looks like some misaligned text here in panel 3:

http://archives.sluggy.com/book.php?cha ... 2008-09-12

Not sure if this is new or a problem with the original strip, but some of the white lettering here is impossible to read:

http://archives.sluggy.com/book.php?cha ... 2008-09-16

Another C.R.A.P. strip that cut off the top:

http://archives.sluggy.com/book.php?cha ... 2008-09-20

Chapter 58

These strips are all cut off or cropped weird:

http://archives.sluggy.com/book.php?cha ... 2008-10-04
http://archives.sluggy.com/book.php?cha ... 2008-10-31
http://archives.sluggy.com/book.php?cha ... 2008-11-02

Chapter 59, Broken

This strip has some of the next strip at the bottom:

http://archives.sluggy.com/book.php?cha ... 2009-01-06

And the next strip looks like it has part of the previous strip's green at the top:

http://archives.sluggy.com/book.php?cha ... 2009-01-07

Same with these two, first strip has artifacts on the bottom, second strip has them on top:

http://archives.sluggy.com/book.php?cha ... 2009-02-10
http://archives.sluggy.com/book.php?cha ... 2009-02-11

This strip has an essay I wrote underneath it! Not a bug report but still very cool. :)

http://archives.sluggy.com/book.php?cha ... 2009-03-23

This strip has some artifacts on top:

http://archives.sluggy.com/book.php?cha ... 2009-04-08

This strip has a blank/empty "Pete's Notes" box underneath it, not sure if something is supposed to be there or not.

http://archives.sluggy.com/book.php?cha ... 2009-04-15

This strip has artifacts on top:

http://archives.sluggy.com/book.php?cha ... 2009-05-26

Undersized strips in Chapter 08:

Only some rows are not showing up at 1150:
http://archives.sluggy.com/book.php?cha ... 1998-09-20

Whole strip is undersized:
http://archives.sluggy.com/book.php?cha ... 1998-10-25

Unfortunately the forums ate my Chapter 61 post. I'll try and recreate it later. For now, Chapter 62:

This strip has something quite weird going on with the top row:

http://archives.sluggy.com/book.php?cha ... 2011-02-25

This strip has artifacts on the bottom:

http://archives.sluggy.com/book.php?cha ... 2011-03-31

More artifacting:

http://archives.sluggy.com/book.php?cha ... 2011-03-31
http://archives.sluggy.com/book.php?cha ... 2011-05-06
http://archives.sluggy.com/book.php?cha ... 2011-05-19

Chapter 64:

Artifacting:

http://archives.sluggy.com/book.php?cha ... 2012-07-04
http://archives.sluggy.com/book.php?cha ... 2012-07-06
http://archives.sluggy.com/book.php?cha ... 2012-10-19
http://archives.sluggy.com/book.php?cha ... 2013-02-26

Chapter 65:

Artifacting:

http://archives.sluggy.com/book.php?cha ... 2013-04-04
http://archives.sluggy.com/book.php?cha ... 2013-06-05
http://archives.sluggy.com/book.php?cha ... 2013-06-06
http://archives.sluggy.com/book.php?cha ... 2013-06-07
http://archives.sluggy.com/book.php?cha ... 2013-09-12
http://archives.sluggy.com/book.php?cha ... 2014-04-22
http://archives.sluggy.com/book.php?cha ... 2014-04-24

Chapter 66:

Not embiggened:

http://archives.sluggy.com/book.php?cha ... 2014-10-23
http://archives.sluggy.com/book.php?cha ... 2014-12-26
http://archives.sluggy.com/book.php?cha ... 2014-12-27
http://archives.sluggy.com/book.php?cha ... 2014-12-28
http://archives.sluggy.com/book.php?cha ... 2014-12-29
http://archives.sluggy.com/book.php?cha ... 2014-12-30
http://archives.sluggy.com/book.php?cha ... 2014-12-31
http://archives.sluggy.com/book.php?cha ... 2015-01-01
http://archives.sluggy.com/book.php?cha ... 2015-01-02
http://archives.sluggy.com/book.php?cha ... 2015-01-03
http://archives.sluggy.com/book.php?cha ... 2015-01-04
http://archives.sluggy.com/book.php?cha ... 2015-01-05
http://archives.sluggy.com/book.php?cha ... 2015-01-06
http://archives.sluggy.com/book.php?cha ... 2015-01-07
http://archives.sluggy.com/book.php?cha ... 2015-01-08
http://archives.sluggy.com/book.php?cha ... 2015-01-09
http://archives.sluggy.com/book.php?cha ... 2015-01-10
http://archives.sluggy.com/book.php?cha ... 2015-01-11

Artifacting:

http://archives.sluggy.com/book.php?cha ... 2014-10-29
http://archives.sluggy.com/book.php?cha ... 2014-12-02
http://archives.sluggy.com/book.php?cha ... 2014-12-05
http://archives.sluggy.com/book.php?cha ... 2015-02-05

Unreadable text:

http://archives.sluggy.com/book.php?cha ... 2015-01-14

Here are some broken strips I've collected. I haven't been doing it systematically at all, but I went through and took any strips Malice found off the list.

http://archives.sluggy.com/book.php?cha ... 2016-09-05 - part of next comic on bottom, irregular border
http://archives.sluggy.com/book.php?cha ... 2014-11-28 - has part of prev. day
http://archives.sluggy.com/book.php?cha ... 2016-02-05 - part of prev. comic
http://archives.sluggy.com/book.php?cha ... 2016-03-02 - white bar at top not supposed to be there?
http://archives.sluggy.com/book.php?cha ... 2016-03-03 - part of prev. comic
http://archives.sluggy.com/book.php?cha ... 2016-03-22 - part of prev. and next comics
http://archives.sluggy.com/book.php?cha ... 2016-03-23 - part of prev. comic
http://archives.sluggy.com/book.php?cha ... 2010-09-28 - part of prev. comic
http://archives.sluggy.com/book.php?cha ... 2016-03-24 - part of next comic
http://archives.sluggy.com/book.php?cha ... 2016-03-25 - part of prev. comic
http://archives.sluggy.com/book.php?cha ... 2016-03-28 - part of prev. comic
http://archives.sluggy.com/book.php?cha ... 2016-03-30 - part of prev. and next comics
http://archives.sluggy.com/book.php?cha ... 2016-04-01 - too small (I think)
http://archives.sluggy.com/book.php?cha ... 2016-04-04 - part of prev. comic
http://archives.sluggy.com/book.php?cha ... 2016-04-26 - part of next comic
http://archives.sluggy.com/book.php?cha ... 2008-09-15 - too small
http://archives.sluggy.com/book.php?cha ... 2008-09-16 - Malice mentioned this one. I'm pretty sure it used to be readable

Chapter 67:

Artifacting:

http://archives.sluggy.com/book.php?cha ... 2015-07-08
http://archives.sluggy.com/book.php?cha ... 2015-10-08

Edit: Nice, FMA!

Yeah it's supposed to have a black outline on that text. Most of the comics in that arc with text that was not black was supposed to be the same. Here's the original for this one:
https://static.sluggy.com/images/comics/080916y.jpg