As requested in this previous Mi Yodeya answer, why is rice considered kitniyot? Pesachim 114b quotes R. Huna as allowing "beet and rice" on the Seder plate in place of the lamb bone and the egg. It seems to me that a ruling in the Talmud ought to have preempted the later Ashkenazi custom.
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It is not the case that a ruling in the Talmud will always overcome any possible custom developed later.
In Talmudic times, there was no customary prohibition of kitniyot. Rav Huna, in the quote, is giving an example of what may be used as the two cooked dishes, even though of course other simple dishes would be fine as well. And he specifies orez (which may very well be millet, rather than rice). And, the gemara explains, this is to the exclusion of the position of Rabbi Yochanan ben Nuri, who maintained that this was a grain, which would present problems of Chametz.
Later, with full knowledge that in previous generations, kitniyot was allowed, and with full knowledge of Rav Huna's statement, various Ashkenazi communities instituted a decree (gezeira) or accepted a custom (minhag) not to consume kitniyot, something which included rice. This, for reasons such as that wheat grains were still present in the fields from the previous harvest.
You could similarly ask how Rabbenu Gershom could decree that a man couldn't give his wife a bill of divorce against her will, or marry multiple wives, when there are explicit Talmudic statements which allow these. The answer in all cases is that your assumptions of what the proper methodology should be is not the same as the methodology with which they were operating.
Kitniyos: The Next Best Thing to Chometz actually has a complete podcast shiur going into the details as to how, when, and why this custom arose among Ashkenaz Jews.