"It was very, very frustrating," said Francis.
"I get [annoyed] when we play these school teams and the referees look after them.
"Some of the decisions he made were unbelievable."
The buildup led to City hesitating on challenges and PNBHS swooped to get the equaliser, and then they went ahead, with Josh Davenport and Jaeden Shaw the goal scorers
"They were passing well, and no-one wanted to go in to make the tackle," said Francis.
"We'd been pinged over, and over, and over.
"The boys didn't want to give away a penalty at the top of the box for another free kick."
The score could have been worse if City's veteran goal keeper Glenn Graham, in his 50's, had not "played out of his skin" to make some big saves.
In the dressing shed afterwards, Francis was still worked up over some of the officiating, before Berry tactfully reminded him the side had not played well enough to overcome it.
"He was right. We need to be accountable for our own actions.
"The second half they came out and moved the ball really well. We didn't react to it well enough."
Bell did not receive enough support up front, while the new-look midfield had not functioned as well as they could have, Francis said.
Since dominating the Premiership from April to May with seven straight wins and 40 goals scored to only one conceded, City have now gone 2-2 in matches since the start of June, with a differential of seven goals scored to six conceded.
It has allowed Hokowhitu FC Rangers to make up the difference, as their 5-1 win over Levin AFC moved them up to a share of the lead with City, separated by a goal differential of only six, which at one time had been in the high double figures.
"We've got to win every game now if we want to win this league - there's no buffer now," said Francis.
With Graham-Luke on suspension for three more games, while Ngaau will be watched carefully at training as simply walking on his injured calves is painful, Francis hopes Hussey at least will be recovered next week and the wider-squad players step up in the tight race.
Meanwhile at Skoglund Park, the GVCA Wanganui Athletic Reserves had their big first round win flipped on them by home side BB Construction North End 1sts, losing 5-1.
Samuel Conley scored Athletic's sole goal, with James Cole getting a double for North End, while David Mccorkindale, Jona Mufunda and Matthew Ward also found the back of the net.