There has been a noted war of words between supporters of Yeshiva University and Yeshivat Chovevei Torah (YCT).
There were the harsh remarks of Howard Jonas about YU at the YCT dinner several years ago. On the other side, Rabbi Herschel Schacter referred to Rabbi Weiss and Rabbi Saul Berman as Amalek.
There is a standoff that appears to have been won by the roshei yeshiva at YU (incl. Rabbi Schacter) to block YCT graduates from joining the RCA (the organization of modern Orthodox rabbis).
The latest flare up began in March 2007 when Rabbi Michael Broyde published an open letter challenging YCT to repudiate Jonas’ 2004 statements. Then Rabbi Natti Helfgott responded by listing the things that YU has done that are far uglier than Jonas’s comments:
-YU administrators calling Orthodox synagogues considering candidates from YCT and pressuring them not to hire the YCT musmach. Leading Orthodox rabbis, including Rabbi Jonathan Rosenblatt, visit Orthodox synagogues considering candidates from YCT and pressure them not to hire the YCT graduates (musmach).
-Rabbi Schachter tried to block YCT musmachim from getting semicha (rabbinic ordination) from the Israeli rabbinate.