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?
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.
There seems to have been regional variation with regards to pronunciation, rather like today.
Eruvin 53b has a whole bunch of anecdotes about such variations. For example:
א"ר אבא אי איכא דמשאיל להו לבני יהודה דדייקי לשני מאברין תנן או מעברין תנן אכוזו תנן או עכוזו תנן ידעי שאילינהו ואמרי ליה איכא דתני מאברין ואיכא דתני מעברין איכא דתני אכוזו ואיכא דתני עכוזו
Rabbi Abba said: If there is anyone who can ask the people of Judea, who are precise in their language, whether the term in the mishna that we learned is me’abberin with an alef or me’abberin with an ayin, he should ask them. Similarly, with regard to the blemishes of a firstborn animal, was the term meaning its hindquarters that we learned in the mishna akkuzo with an alef, or did we learn akkuzo with an ayin? They would know.
Someone asked the people of Judea, and they said to him: Some teach me’abberin with an alef, and some teach me’abberin with an ayin. Some teach akkuzo with an alef, and some teach akkuzo with an ayin. Both versions are well founded and neither one is erroneous.
בני גליל דלא דייקי לישנא מאי היא (דתניא) דההוא בר גלילא [דהוה קאזיל] ואמר להו אמר למאן אמר למאן אמרו ליה גלילאה שוטה חמר למירכב או חמר למישתי עמר למילבש או אימר לאיתכסאה
As to the people of the Galilee, who are not precise in their speech. What is the meaning of this? As it was taught in a baraita, that there was a certain person from the Galilee who would walk and say to people: Who has amar? Who has amar? They said to him: Foolish Galilean, what do you mean? Galileans did not pronounce the guttural letters properly, so it was unclear whether he sought a donkey [ḥamor] to ride, or wine [ḥamar] to drink, wool [amar] to wear, or a lamb [imar] to slaughter.