Not much to say here other than a Quality Control problem.
If the cover is misaligned during binding, it can have have a bad wrap on the book.
The trim could run high or low causing additional problems.
By "wrap" I mean how the black line dividing the front and back cover not falling perfectly on the spine.
Now for something you might not know...
This is a problem that is much more common in the Bronze Age than any other age.
If you've ever seen a book where the spine line lays perfectly on the spine, but the "Marvel Comics Group" banner runs slightly diagonal compared to the top edge of the book.
One possibility is that the trim of the book is skewed (the sides are not a perfect 90 degrees from the others).
However, if you see this to be an extremely common flaw on a particular book, it's quite possible the Original Artwork itself is skewed.
Example below...
The red lines are perfectly parallel, but look at the lines that make up the "King-Sized Annual" banner.
This is common on a lot of books from the Bronze Age.
Marvel Spotlight #5, and Ghost Rider #1 (Two of my favorites) have this problem.
And it all goes back to the original art.
I have no idea why some of the covers were built this way, and some were not.
I would just add, having been a commercial artist and understanding the old method of paste up and layout, that a lot of the stuff on the covers were pasted on. Common elements of the covers such as the logo were photocopied and pasted to either the original artwrork or a copy of it before the photographic plate making process. This is how the uniform look of the logo is maintained over the course of many years and dozens of issues.
So one of a few things can happen to create the crooked appearance of the banners on some covers. First is that the fixative used was the repositionable type which is the case most of the time. This allows for correcting the position of the piece without tearing up the art. So it is possible that the pasted element shifted during transport to the camera, photocopy machine or printer. The second is that a lot of times it would be some office production assistant or other non-artist or someone in a great hurry that would paste these items onto the artwork. In this case, carelessness or lack of experience might cause this issue.