"Didn't play well enough," said Francis, who himself took the field for the last 15 minutes.
"We just made mistakes at the wrong end of the park, gave the ball away, didn't track back, couldn't hit feet.
"Just basic mistakes to be fair. It was a pretty average performance."
City opened the scoring through Latham Berry but Red Sox replied to head into half time at 1-1.
The visitors then ran out to lead 3-1 in the second half before City's Dan Aplin narrowed the margin late in the game.
"It just didn't look like we were up for it. I don't know where their mindset is," Francis said of his players.
"Red Sox are humming, mate. They just beat the team on the top of the league and we just made it very hard for ourselves.
"They came out in the second half a lot more urgent than we did and not everybody was working.
"They didn't press us into making mistakes, we just made out own mistakes. We got what we deserved."
City play eighth place North End in Palmerston North next week.