The midfielder featured for the U23s yesterday.
"It is very easy to explain why he is not playing," said Benitez. "You have Longstaff and Hayden doing well. Still you have Ki and Diame - they were ahead of him - and they are not in the team, so you have five midfielders now for two positions.
"We don't have the the space - physically, you cannot put more than 18 players in the squad. Someone has to stay out and that is my problem to decide."
Benitez added: "Many people say, 'Yeah, but Jonjo could be…'. Yes, 'could be', but we are doing well."