oomis – I believe you got it backwards. Think “Vayoled ben”.
I didn’t get it backwards. Remember, the Torah DOES NOT come with nekudos. People put them in, so if it is pronounced for some reason as ben, as per your example, that may be due to the way we have accepted pronouncing it in that instance. Generally speaking, from a strictly grammatical point of view, Bein is translated as “son” and Ben (as in Yosef ben Yaakov) means the “bein” of someone (though hopefully not the “bane” of anyone). It is typically written with a tzeireh under the beis, and not a sergol (I think that is the correct name for the three dots that vocalize as a short “e”, though I always said seh-gol as a child). BTW, sometimes vowels are altered because of some OTHER grammatical rule that comes before or after a particular word.