Hughton’s side put up a much better performance compared to their opening-day defeat to Cape Verde but were undone by defensive mistakes.
West Ham star Mohammed Kudus scored twice but mistakes at the back by Inaki Williams and Osman Bukari allowed Egypt to tie the game.
Addressing journalists after the game, Hughton said it was frustrating to see his side only pick up a point after their gallant performance.
The 65-year-old also commended the commitment and fight displayed by his, adding that he could not fault any of them.
“Of course, it's very frustrating because I thought we deserved to win the game,” the Black Stars boss said.
“What I asked after the first performance against Cape Verde from the players was a better performance. More commitment and more running to give ourselves a better chance of putting in a performance to win this game. I don't think I can fault the players, their attitude and the way they applied themselves.”
The Black Stars had a good chance to move to the top of Group B but were undone by defensive blunders against the Pharaohs.
Kudus seemed destined to give Ghana all three points after passing a late fitness test to be named in the starting line-up.
But despite scoring a double, the West Ham star’s efforts were not enough as Egypt twice came back from a goal down to salvage a draw, thanks to goals from Omar Marmoush and Mostafa Mohamed.
The result leaves Ghana winless in Group B and also at the bottom of the group, which places more importance on their final group game against Mozambique.