Why didn't EDITH recognise Quentin, who was a former employee under Tony Stark?
We don't know...
However, your question assumes that EDITH had access to this information. Insofar as EDITH was intended for Peter's use there's no particular reason why she should have lists of ex-employees on hand. There must be some limits to the amount of information she has on hand.
Why didn't EDITH inform Peter that Mysterio is actually a former Stark industries employee who was fired by Stark and not some guy from another Earth?
Given the above and even assuming that she did recognise Beck he's supposedly from another Earth.
There's no reason why there couldn't be a Quentin Beck on this Earth AND another (Mysterio) on another Earth.
So even if she did recognise him, he has an easy explanation that he's a DIFFERENT Quentin Beck.