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On the Wikipedia page of מנשה מאיליה it says:

לפעמים סבל מקנאים שלא ירדו לסוף דעתו. היו שהסתייגו ממנו בגלוי כגון הרב יעקב'קע לנדא (בנו של הרב יחזקאל לנדא, בעל הנודע ביהודה), שעורר קפידא בגלל שהשיג על פירוש רש"י. ואף ביקשו להחרים אותו, אך קרוביו וידידיו (בהם הרב יהושע צייטלין מחכמי שקלוב) הגנו עליו והחרמות לא הוטלו. גם הגר"א הגן עליו כמה פעמים מפני רבנים שביקשו להצר לו

Roughly:

Sometimes he suffered from zealots who did not fully understand him. Some explicitly expressed their reservations, like Rabbi Jakey Landau (the son of Rabbi Ezekiel Landau, author of Noda Bihuda), who protested because he had dissented from Rashi's commentary. They even sought to excommunicate him, but his relatives and friends (among them Rabbi Joshua Zeitlin, among the wise men of Shkloŭ) shielded him, and the bans were not set. The Vilna Gaon also shielded him, several times, from the rabbis who had sought to constrict him.

Where is this disagreement with Rashi that the son of the Nodah BeYehudah tried to put him into cherem for?

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