“Splitting the atom,” it turns out, is what one might call an etymological oxymoron — “atom” comes from the Greek “a-,” meaning “not,” and “tomos,” meaning cut. The atom was that which couldn’t be split, at least through chemical processes, but it turns out that it can be split through nuclear processes (whether generated by humans or stemming from natural radioactivity).
Likewise with “gym clothes,” since “gymnasium” comes from the Greek verb meaning “to train in the nude.” And “jumbo shrimp” indeed qualifies, since shrimp seems to come from an Old English term meaning “to shrink.”
What other examples are there? Please note them in the comments, and quote the relevant etymology from some credible source (preferably a dictionary).