I suspect that Tolkien's "defects" were things such as timelines, names, small deviations in stories, etc. There are several notes in the HoME series where you can see that the stories of the first age as sketched out and presented are somewhat different from what was finally published in the LotR. There are also minor variations in dating the Numenorean kings, for example. There may be other inconsistencies, but I would warrant they would not be caught by the casual reader.
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"Alas, poor Yorick! I knew him, Horatio; a fellow of infinite jest, of most excellent fancy."
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