In the portion read for Parshas Zachor we find the commandment תמחה את זכר עמלק, wipe out the remembrance of Amaleik. The gemara (בבא בתרא כא) relates a rather bizarre incident where Yoav, David HaMelech's general was sent to destroy Amaleik. He returns, having wiped out all of the males. When he is confronted by David HaMelech as to why the others were allowed to live, he declares that he was taught "Timcheh es zachar Amaleik," wipe out the males of Amaleik. Needless to say, Yoav was not very happy when he found out he had been taught wrong.
It is indeed quite difficult to understand how the mesorah could be so skewed as to totally misunderstand and misrepresent this pasuk. I heard an interesting insight into this mistake from the footnotes of the מעשה רב. Yoav's rebbe never thought that the word was pronounced "zachar." Rather, this error was a result of a misunderstanding of the possessive form of zachar."
The word for smoke is "ashan." The vowelization of this word is the same as "zachar." However, when the Torah describes Har Sinai and describes how its smoke rose like the smoke of a furnace, the term used is "eshen hakivshan." Clearly, when the word "ashan" is used in the possessive, both kamatzim are converted to segolim. Yoav's rebbe read the pasuk "timche es zecher Amaleik," and understood that zecher was the possessive form of zachar. He therefore mistakenly taught Yoav that the commandment is to wipe out only the males of Amaleik.