Yes, there are countless instances of rabbis (from Talmudic times to the present) disagreeing on a wide range of halachic (legal) and hashkafic (theological) issues.
As an example, Rabbi Natan Slifkin has demonstrated that dozens of Rishonim (medieval rabbis) argued that Chazal (the rabbis of the Mishnah and Talmud) erred in scientific matters, because they were relying on the science of their time, rather than a scientific oral tradition from Mount Sinai. Other Rishonim disagreed (some believed that Chazal only appeared to be incorret about some scientific matters, because nature had changed.)
Today, many charedi rabbis dispute Rabbi Slifkin's approach (the book was banned by some prominent rabbis), and maintain that Chazal were definitely right about science and everything else. I don't know whether these rabbis explicitly disagree with those rishonim who believed Chazal erred, as opposed to interpreting them in a different way (or more ambiguously, saying "they can say it; we cannot.") But Modern Orthodox Jews are less likely to have problems with Rabbi Slifkin's approach (and thus with those rishonim who held Chazal erred in science).