The Magpies manager saw his side fall behind after just five minutes. Kiwomya's men were without a game last weekend and more than a week's worth of preparation went down the drain with Luke Chadwick's early goal.
Shaun Williams curled in a fine 25-yard free-kick before half-time but the visitors improved after the break and Callum McGregor handed them a lifeline when he raced clear to slot the ball past goalkeeper David Martin in the 76th minute.
But Patrick Bamford rammed in a loose ball at the death for his sixth goal of the season to leave the Magpies rooted to the bottom of the table and still without a league win.
"I was disappointed in our first half performance," said Kiwomya. "You plan for 10 days how to play against a team then after three or four minutes you're 1-0 down and battling against it.
"It's not great play by them, they haven't cut us open with loads of passes - it's a mistake in defence and they capitalised on it. Then after that you can see the confidence drain out of them and we lose another goal.
"So we got in and said some harsh words to them at half-time and made some changes. In the second half we had a mountain to climb but we managed to get back in it.
"However, I'm very disappointed with the first half because you can't come to clubs like this and go one and two-nil down because you're always going to get beaten.
"I'm upset because we're up against it and we need a win. I'm not saying the players laid down but they've got to do better than that."