Volume II of Frege's Grundgesetze der Arithmetik (Basic Laws of Arithmetic) had already been sent to the press when Bertrand Russell informed him that what we now call "Russell's paradox" could be derived from one of his basic laws. I do not know to what extent Frege's work was known and publicly accepted (volume I was published 10 years before volume II), but this seems a clear case where a major body of work was undermined "from below", to use the words of the OP.

Upon learning of Russell's observation, Frege quickly wrote up an appendix to volume II, where he writes, "Hardly anything more unfortunate can befall a scientific writer than to have one of the foundations of his edifice shaken after the work is finished. This was the position I was placed in by a letter of Mr. Bertrand Russell, just when the printing of this volume was nearing its completion." (This translation appears in the Wikipedia article.)