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 ...
Some names are popularly used in a different form than the way they're spelled or pronounced in Tanach. A few that I can think of are: Nochum (נָחוּם) - is written in Tanach (Nah. 1:1) as נַחוּם ...