Given the antisemitic issues in the Labour party, and the increased scrutiny on what precisely politicians say, or have said, and that this involves the leader of the Labour party, I can see that Jewish people might justifiably be sensitive to what, for most of us, would be an unusual pronunciation of Epstein (thinking of say, Brian Epstein).
Unless he explains himself, and it would be good to know if he had pronounced the name differently before, my guess is that he was probably trying to show that he was aware of how Jewish people might pronounce this name but was unaware that by doing so he could be seen as either being patronising or was highlighting the Jewishness of Epstein.