In Shabbos 77a-77b, Chazal ask about the spelling of a series of words, questioning whether the words are spelled with an alef - as in גראינין - or with an ayin - as in גרעינין. Wasn't ayin vocalized at that time? If so, how could there be a question when the two letters had markedly different pronunciations?
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I don't know how these words are said, I'm guessing the vowelization is גַרְעִינִין or גַרְעֵינִין or maybe גַרְעֵינְיָן?
Either way, unless you're trying to be particularly makpid on pronunciation, ayin-tsere-malei or ayin-hirik-malei sound a lot like their aleph-based counterparts.
Languages also tend to be forgiving when there's no easily-confusable near-homonym.
In addition, Sumerian doesn't have an ayin sound, so perhaps Eastern Aramaic didn't pronounce their ayins as clearly as Western Aramaic.
EDIT: Here's a pdf that (I think) is trying to explain that there is a shift between aleph and ayin in Jewish Middle Aramaic, so it seems like things were confused at the time.
Perhaps these words that Chazal are asking about were not words used on a daily basis and therefore it was unclear how to pronounce them.