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?
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.
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.