Did Itachi know that Shisui had a Mangekyo Sharingan?
It is not a plot hole. And he isn't necessarily wrong. He just meant the third person alive. Of course he knew about Shisui, he had his eye. Of course he knew about Izuna and Madara too since he introduced their story to Sasuke. And he probably knew about other unnamed Uchihas too, if there were any, because as he said the Uchihas were killing their best friends for decades to achieve it. So I can't find any other logical explanation.