Why do we call it masechet Beitza now, and not masechet Yom Tov, as was apparently once common? Unlike the parshiot, which are named after their first words, masechtot are all named after topics, except Beitza. This is particularly odd considering that today, many people actually call it "Bei'a" to avoid a word not appropriate for mixed company. So why not just call it "Yom Tov"?
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See the beginning of Rabbenu Chananel on Masseches Beitzah, where he - or whomever copied the manuscript the printed text is based on - began it with the following rhyming ditty:
אתחיל מסכת ביצה בעזרת גדול העיצה
Maybe because "Yom Tov" just sounds like too generic a name? There are, after all, several other masechtos that discuss, and/or are named for, specific Yamim Tovim.
One of the reasons we call the Mesechta Beiya and not Beitza is in order to avoid any errors. The Gemara in Sanhedrin, daf 5, tells of an occasion when Rebbe came to a city and the people were kneading their doughs in water that was tamei. They explained that a learned man had once taught them that 'water of Betzayim does not allow it to become tamei'.
After investigating, it turned out that this talmid chacham has said 'water of Beitzim' - meaning water of eggs — not Betzayim (pond water), and the people of the town took it to mean water from the pond.
To avoid further confusion---and resulting halchic transgression---between the two similar words, people began pronouncing it 'Beiya'.