As far as I understand it, Wertham's proof that comic books caused delinquency was based upon the fact that he interviewed a large number of delinquents and asked them if they read comics.
He did not use control groups or interview a general cross-section of the juvenile population. As most children at the time read comics it was hardly surprising that most of the delinquents he interviewed did.
There have been several instances of comics being published without the stamp (in at least one case because it fell off the original of the cover and no-one noticed).
Particularly, three issues of Spiderman published in 1971 that showed a character on drugs (though in a very negative manner) did not carry the stamp. This actually led to a modification of the code.
Also Swamp Thing had the stamp permanently removed when the Authority actually read an issue and discovered what they had been rubber stamping for months. DC Comics simply refused the rewrites, removed the stamp, and never submitted another issue of Swamp Thing.
The strangest ruling by the authority that I know of is regarding the artist Kevin O'Neill, a Brit who worked in 2000 AD and various American comics including Marshall Law. Most recently he drew the League of Extraordinary Gentlemen (written by Alan Moore). The Comics Code Authority basically said at one point that his artistic style was totally unacceptable and they would not pass any book which he drew.