Rafael Benitez has taken 22 points from his 13 Premier League games at Chelsea this season, two fewer than Roberto Di Matteo did from his 12 matches in charge (24).
"I think there were too many mistakes. I could see a red card that was not shown for Coloccini," said Benitez.
"So we had a chance, he [Demba Ba] had the ball, he received a kick and got a broken nose, it was bleeding. It was so simple, if it was in the middle of park you would go back and give a free-kick.
"It is very simple and very clear - penalty and red card because it was a chance. It's a strange rule and the penalty could have changed everything."
Ba had to be withdrawn before half-time and Jonas Gutierrez then put Newcastle ahead, but Chelsea responded well in the second half, taking a 2-1 lead through fantastic strikes by Frank Lampard and Juan Mata.
But Newcastle's Moussa Sissoko scored twice to earn the Magpies back-to-back victories and extend Chelsea's winless streak to four games.
Alan Pardew on 'unbelievable' Newcastle victory over Chelsea
Benitez has gained 24 points from 13 Premier League games in charge this season, which is two less than former boss Roberto Di Matteo accrued in 12 games before he was sacked in November.
Interim boss Benitez said his team had to "manage the pressure" but his side were naive in allowing Newcastle to counter-attack.
"The reaction of our team in the second half was fantastic," Benitez told BBC Sport.
"We were reacting really well, we scored two goals, the team was doing really well.
"But we gave them the opportunity to play counter-attack so we have to have more experience, but there were still too many [refereeing] incidents that were too difficult to explain."
This page is best viewed in an up-to-date web browser with style sheets (CSS) enabled. While you will be able to view the content of this page in your current browser, you will not be able to get the full visual experience. Please consider upgrading your browser software or enabling style sheets (CSS) if you are able to do so.