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Actually the holes are created by a "Former".
Which would be the piece of equipment at the end of the Press that folds and stacks the printed book into raw untrimmed books that are ready to go to the Bindery.
It uses pins on a "Gripper" to grab the edge of the books, thus creating the little holes you see.

These raw books are then taken to the Bindery where they get the cover attached to the body, stapled, and trimmed.
The holes are meant to be trimmed off, but if there is any variance in the "press roll" or "bindery trim", they actually fall inside of the trimmed area.
This is a pretty common problem in some comics.

The reason it may be more common on a particular book, could be...
1) *Equipment* There is an equipment malfunction that may not severe enough to repair until there is downtime in the schedule. Usually as long as the press keeps printing with no major problems, they keep it running.
2) *Quality Control* That particular book could have been printed by a Pressman that had the pinholes too far out of spec. Thus a good portion of the copies were printed with the holes too far into the live area for the Bindery to trim them out without over trimming the book (Making the book shorter).
3) *Quality Control* The Binder could have the trim depth set too shallow on the edge where the pinholes are. As the problem before, it may be noticed and corrected quickly, or could go unnoticed for hours by an unattentive Bindery Operator.

There could be other reasons, but I'd bet the listed ones would be within 99% accuracy.
Bottom line...Common production flaw.

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The Printer crease is caused by the paper getting a wrinkle in it as it passes through the press units.
The units smash the wrinkle flat while printing the images onto the paper.
There is no ink on the inside of the wrinkle as this area was "hidden" during the print process.
If you have a cheap book with this type of wrinkle, you can try to unfold this wrinkle area and reveal the white paper area.
Do this only if you want to see what I'm trying to describe.
I wouldn't do this to a high grade or valuable book because you will end up with a white streak running through the cover.

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Something I'd like to add to my response...
This is more common with thinner, cheaper paper.
It can also be caused after the ink is printed on the paper as it goes through the rollers at the end of the press.
If there is ink inside of the crease, it was caused after it was inked.
If there is no ink inside of the crease, it was caused before ink hit the page.
More often than not, it will be before inked.

This is very typical on specific books because the cover paper was cheap or very thin (Low basis weight).
Weird War #1 and Defenders #1 come to mind as books with a high percentage of this flaw.
Actually, Greggy pointed out to me that it is very hard to find a Weird War #1 without a Print Crease.
I have looked at many copies since he told me this to find that he is correct.

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Crooked, warped squarebound!

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Miscuts! (Book not cut squarely)

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I'll get back on this one with an illustrated explanation.
It may take a while.

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Spine puckering! on GS and square bound books. . . you da' man Dice!

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Answered above in response to Greggy.