Teenager Pappoe had only been on the pitch four minutes when he lunged in after the whistle had been blown for a throw-in and Parkinson thought the challenge could have seriously hurt Yeates.
Jeffrey Monakana, signed on loan from Preston this week, scored one goal and made the other as Colchester came back from 1-0 down to take a 2-1 half-time lead.
But Bermuda international striker Nahki Wells scored his second goal of the match - his ninth of the season - to earn Bradford a point.
Parkinson said: "I thought the whistle had gone and the game had stopped.
"Pappoe came out of nowhere and lunged himself in. I don't know what he was thinking about - the game had stopped. I thought Mark Yeates had broken his leg. It certainly shook him up. He looks ok, but we will look again on Sunday morning."
Parkinson was impressed with his old club, adding: "I have seen the DVDs of their games and barring last week at Coventry I thought they were one of the best teams I have seen.
"They have got some dangerous players and were always threatening on the break.
"I thought we started in great fashion and scored and maybe thought that we would go to score a second and a third.
"Maybe that cost us, but I can't fault the way we responded after going behind. We said at half-time we had to give everything we had got and try to get back in the game, which we did when Nahki Wells equalised for us and we could have won after that."
Wells put Bradford in front after 14 minutes, the ball falling into his path from an attempted clearance by David Wright and he spun past Tom Eastman to slot the ball into the net.
But the lively visitors crowned a strong spell of pressure with two goals in four minutes. Monakana equalised after 28 minutes with an angled shot into the far corner after taking a pass from Craig Eastmond - the first time Bradford had conceded a goal at home this season.
Colchester went ahead after 32 minutes when Monakana's through pass split the Bradford defence and Jabo Ibehre fired past the advancing Jon McLaughlin.
Wells equalised with his second goal of the match in the 52nd minute when his looping back header from left-back James Meredith's cross deceived goalkeeper Sam Walker as the ball floated in the far corner.
Both sides went close in an exciting finale with Massey hitting the post and Walker turning a goalbound shot from Wells over the crossbar.